Bioconductor Code: Browse

Browse code

bump x.y.z version to odd y following creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:05:31
Showing 1 changed files

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.46.0
                                     +Version: 1.47.0
                                      Date: 2019-10-12
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:05:31
Showing 1 changed files

DESCRIPTION

History View file @ d15d8fa

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.45.0
                                     +Version: 1.46.0
                                      Date: 2019-10-12
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

Compatibility with Rhtslib 1.99.1

Daniel C. Jones authored on 03/10/2022 16:36:34
Showing 1 changed files

DESCRIPTION

History View file @ 882be9e

@@ -7,11 +7,11 @@ Description: This package implements a model of per-position sequencing
                                              bias in high-throughput sequencing data using a simple Bayesian
                                              network, the structure and parameters of which are trained on a
                                              set of aligned reads and a reference genome sequence.
                                     -Author: Daniel Jones <dcjones@cs.washington.edu>
                                     -Maintainer: Daniel Jones <dcjones@cs.washington.edu>
                                     +Author: Daniel Jones <djones3@fredhutch.org>
                                     +Maintainer: Daniel Jones <djones3@fredhutch.org>
                                      Depends: R (>= 3.0.2), GenomicRanges (>= 0.1.0), Biostrings (>=
 .15.0), methods
                                     -LinkingTo: Rhtslib (>= 1.15.3)
                                     +LinkingTo: Rhtslib (>= 1.99.1), zlibbioc
                                      SystemRequirements: GNU make
                                      Suggests: Rsamtools, ggplot2
                                      LazyLoad: yes

Browse code

bump x.y.z version to odd y following creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:06:44
Showing 1 changed files

DESCRIPTION

History View file @ b471f9a

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.44.0
                                     +Version: 1.45.0
                                      Date: 2019-10-12
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:06:44
Showing 1 changed files

DESCRIPTION

History View file @ 59a8fc9

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.43.0
                                     +Version: 1.44.0
                                      Date: 2019-10-12
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump x.y.z version to odd y following creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 15:57:52
Showing 1 changed files

DESCRIPTION

History View file @ b3b6bc6

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.42.0
                                     +Version: 1.43.0
                                      Date: 2019-10-12
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 15:57:52
Showing 1 changed files

DESCRIPTION

History View file @ e8ef6fa

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.41.0
                                     +Version: 1.42.0
                                      Date: 2019-10-12
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump x.y.z version to odd y following creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 15:47:09
Showing 1 changed files

DESCRIPTION

History View file @ b5c22b2

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.40.0
                                     +Version: 1.41.0
                                      Date: 2019-10-12
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 15:47:09
Showing 1 changed files

DESCRIPTION

History View file @ c9d8e78

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.39.0
                                     +Version: 1.40.0
                                      Date: 2019-10-12
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump x.y.z version to odd y following creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 14:39:54
Showing 1 changed files

DESCRIPTION

History View file @ f9b6f07

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.38.0
                                     +Version: 1.39.0
                                      Date: 2019-10-12
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 14:39:54
Showing 1 changed files

DESCRIPTION

History View file @ b5490ca

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.37.1
                                     +Version: 1.38.0
                                      Date: 2019-10-12
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

Call Rscript instead of R in Makevars

This is just for conformance with the "Writing R Extensions" manual
which recommends to use `"${R_HOME}/bin${R_ARCH_BIN}/Rscript"` rather
than `"${R_HOME}/bin/R" --vanilla --slave` for running R code in
Makevars files.

Hervé Pagès authored on 14/07/2020 20:41:22
Showing 1 changed files

DESCRIPTION

History View file @ ddd3af8

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.37.0
                                     +Version: 1.37.1
                                      Date: 2019-10-12
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump x.y.z version to odd y following creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:24:05
Showing 1 changed files

DESCRIPTION

History View file @ abd9738

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.36.0
                                     +Version: 1.37.0
                                      Date: 2019-10-12
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:24:04
Showing 1 changed files

DESCRIPTION

History View file @ 2b49d14

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.35.0
                                     +Version: 1.36.0
                                      Date: 2019-10-12
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump x.y.z version to odd y after creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:35:22
Showing 1 changed files

DESCRIPTION

History View file @ e80a73b

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.34.0
                                     +Version: 1.35.0
                                      Date: 2019-10-12
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:08:18
Showing 1 changed files

DESCRIPTION

History View file @ 9d5b1f7

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.33.1
                                     +Version: 1.34.0
                                      Date: 2019-10-12
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

Adjust Makevars to work with latest Rhtslib

Hervé Pagès authored on 12/10/2019 20:57:09
Showing 1 changed files

DESCRIPTION

History View file @ 881ab3e

@@ -1,6 +1,6 @@
                                      Package: seqbias
                                     -Version: 1.33.0
                                     -Date: 2019-03-15
                                     +Version: 1.33.1
                                     +Date: 2019-10-12
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data
                                      Description: This package implements a model of per-position sequencing
@@ -12,6 +12,7 @@ Maintainer: Daniel Jones <dcjones@cs.washington.edu>
                                      Depends: R (>= 3.0.2), GenomicRanges (>= 0.1.0), Biostrings (>=
 .15.0), methods
                                      LinkingTo: Rhtslib (>= 1.15.3)
                                     +SystemRequirements: GNU make
                                      Suggests: Rsamtools, ggplot2
                                      LazyLoad: yes
                                      License: LGPL-3

Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 16:11:01
Showing 1 changed files

DESCRIPTION

History View file @ f0cc475

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.32.0
                                     +Version: 1.33.0
                                      Date: 2019-03-15
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 15:53:21
Showing 1 changed files

DESCRIPTION

History View file @ edc384f

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.31.1
                                     +Version: 1.32.0
                                      Date: 2019-03-15
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

Update for Rhtslib compatibility. (Patch by Hervé Pagès)

Daniel C. Jones authored on 22/03/2019 20:05:41
Showing 1 changed files

DESCRIPTION

History View file @ 30d6f83

@@ -1,6 +1,6 @@
                                      Package: seqbias
                                     -Version: 1.31.0
                                     -Date: 25-12-2010
                                     +Version: 1.31.1
                                     +Date: 2019-03-15
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data
                                      Description: This package implements a model of per-position sequencing
@@ -9,10 +9,9 @@ Description: This package implements a model of per-position sequencing
                                              set of aligned reads and a reference genome sequence.
                                      Author: Daniel Jones <dcjones@cs.washington.edu>
                                      Maintainer: Daniel Jones <dcjones@cs.washington.edu>
                                     -Depends: R (>= 2.13.0), GenomicRanges (>= 0.1.0), Biostrings (>=
                                     +Depends: R (>= 3.0.2), GenomicRanges (>= 0.1.0), Biostrings (>=
 .15.0), methods
                                     -LinkingTo: Rsamtools (>= 1.19.38)
                                     -Imports: zlibbioc
                                     +LinkingTo: Rhtslib (>= 1.15.3)
                                      Suggests: Rsamtools, ggplot2
                                      LazyLoad: yes
                                      License: LGPL-3

Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:54:29
Showing 1 changed files

DESCRIPTION

History View file @ 2d01265

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.30.0
                                     +Version: 1.31.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:41:47
Showing 1 changed files

DESCRIPTION

History View file @ 498bb37

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.29.0
                                     +Version: 1.30.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:41:38
Showing 1 changed files

DESCRIPTION

History View file @ 9703824

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.28.0
                                     +Version: 1.29.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:35:16
Showing 1 changed files

DESCRIPTION

History View file @ 71ea389

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.27.0
                                     +Version: 1.28.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:52:11
Showing 1 changed files

DESCRIPTION

History View file @ b0502e5

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.26.0
                                     +Version: 1.27.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:39:32
Showing 1 changed files

DESCRIPTION

History View file @ 15c3c25

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.25.0
                                     +Version: 1.26.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump x.y.z versions to odd y after creation of 3_5 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@129129 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:50:57
Showing 1 changed files

DESCRIPTION

History View file @ 0fdf7e7

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.24.0
                                     +Version: 1.25.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump x.y.z versions to even y prior to creation of 3_5 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@129126 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:25:24
Showing 1 changed files

DESCRIPTION

History View file @ 0c35c25

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.23.0
                                     +Version: 1.24.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump x.y.z versions to odd 'y' after creation of 3_4 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@122712 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 19:10:43
Showing 1 changed files

DESCRIPTION

History View file @ 67b8cac

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.22.0
                                     +Version: 1.23.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump x.y.z versions to even 'y' prior to creation of 3_4 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@122710 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 18:45:06
Showing 1 changed files

DESCRIPTION

History View file @ fb81db2

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.21.0
                                     +Version: 1.22.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

bump version after creating 3.3 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@117081 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/05/2016 21:30:44
Showing 1 changed files

DESCRIPTION

History View file @ b9ac733

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.20.0
                                     +Version: 1.21.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

Bump versions prior to creation of 3.3 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@117079 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/05/2016 21:20:18
Showing 1 changed files

DESCRIPTION

History View file @ 51526cc

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.19.0
                                     +Version: 1.20.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

Bumped version number of all packages after creation of 3.2 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@109592 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2015 19:59:53
Showing 1 changed files

DESCRIPTION

History View file @ 98487b5

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.18.0
                                     +Version: 1.19.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

Bumped versions of all packages prior to creating 3.2 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@109589 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2015 19:36:05
Showing 1 changed files

DESCRIPTION

History View file @ c1ec952

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.17.0
                                     +Version: 1.18.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

Bump versions in trunk after creation of 3.1 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@102594 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 16/04/2015 20:02:44
Showing 1 changed files

DESCRIPTION

History View file @ 0262485

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.16.0
                                     +Version: 1.17.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

Bump versions prior to creating 3.1 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@102591 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 16/04/2015 19:42:01
Showing 1 changed files

DESCRIPTION

History View file @ 7ded197

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.15.4
                                     +Version: 1.16.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

add r_arch consideration for Linux

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@100943 bc3139a8-67e5-0310-9ffc-ced21a209358

Nathaniel Hayden authored on 20/03/2015 18:42:12
Showing 1 changed files

DESCRIPTION

History View file @ c011178

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.15.3
                                     +Version: 1.15.4
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

initialize pseudocount member outside of class def

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@100176 bc3139a8-67e5-0310-9ffc-ced21a209358

Nathaniel Hayden authored on 04/03/2015 01:16:09
Showing 1 changed files

DESCRIPTION

History View file @ a93b2a0

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.15.2
                                     +Version: 1.15.3
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

update to require proper Rsamtools version

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@99942 bc3139a8-67e5-0310-9ffc-ced21a209358

Nathaniel Hayden authored on 27/02/2015 20:02:54
Showing 1 changed files

DESCRIPTION

History View file @ 6511256

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.15.1
                                     +Version: 1.15.2
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data
@@ -11,7 +11,7 @@ Author: Daniel Jones <dcjones@cs.washington.edu>
                                      Maintainer: Daniel Jones <dcjones@cs.washington.edu>
                                      Depends: R (>= 2.13.0), GenomicRanges (>= 0.1.0), Biostrings (>=
 .15.0), methods
                                     -LinkingTo: Rsamtools (>= 1.19.36)
                                     +LinkingTo: Rsamtools (>= 1.19.38)
                                      Imports: zlibbioc
                                      Suggests: Rsamtools, ggplot2
                                      LazyLoad: yes

Browse code

update to reflect new Rsamtools recommendations

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@99905 bc3139a8-67e5-0310-9ffc-ced21a209358

Nathaniel Hayden authored on 27/02/2015 01:47:48
Showing 1 changed files

DESCRIPTION

History View file @ 32d20a6

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.15.0
                                     +Version: 1.15.1
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data
@@ -11,7 +11,7 @@ Author: Daniel Jones <dcjones@cs.washington.edu>
                                      Maintainer: Daniel Jones <dcjones@cs.washington.edu>
                                      Depends: R (>= 2.13.0), GenomicRanges (>= 0.1.0), Biostrings (>=
 .15.0), methods
                                     -LinkingTo: Rsamtools
                                     +LinkingTo: Rsamtools (>= 1.19.36)
                                      Imports: zlibbioc
                                      Suggests: Rsamtools, ggplot2
                                      LazyLoad: yes

Browse code

Bumping versions after creating 3.0 release branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@95443 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2014 21:47:41
Showing 1 changed files

DESCRIPTION

History View file @ ea983ab

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.14.0
                                     +Version: 1.15.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

Bump package versions prior to creating the 3.0 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@95439 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2014 21:38:33
Showing 1 changed files

DESCRIPTION

History View file @ b750aaf

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.13.0
                                     +Version: 1.14.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

Second version bump after creating 2.14 release branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@88840 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 11/04/2014 21:21:21
Showing 1 changed files

DESCRIPTION

History View file @ 0b7a015

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.12.0
                                     +Version: 1.13.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

First version bump prior to creating 2.14 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@88838 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 11/04/2014 21:07:21
Showing 1 changed files

DESCRIPTION

History View file @ 58bb009

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.11.3
                                     +Version: 1.12.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data

Browse code

Modify biocViews to remove duplicate biocViews

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@87076 bc3139a8-67e5-0310-9ffc-ced21a209358

Sonali Arora authored on 05/03/2014 00:11:04
Showing 1 changed files

DESCRIPTION

History View file @ 00d798d

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.11.2
                                     +Version: 1.11.3
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing
                                              data
@@ -16,4 +16,4 @@ Imports: zlibbioc
                                      Suggests: Rsamtools, ggplot2
                                      LazyLoad: yes
                                      License: LGPL-3
                                     -biocViews: Sequencing, Sequencing
                                     +biocViews: Sequencing

Browse code

modify to new biocViews to DESCRIPTION file

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@87035 bc3139a8-67e5-0310-9ffc-ced21a209358

Sonali Arora authored on 04/03/2014 22:12:21
Showing 1 changed files

DESCRIPTION

History View file @ 52f122e

@@ -1,19 +1,19 @@
                                      Package: seqbias
                                     -Version: 1.11.1
                                     +Version: 1.11.2
                                      Date: 25-12-2010
                                     -Title: Estimation of per-position bias in high-throughput sequencing data
                                     -Description: This package implements a model of per-position sequencing bias in
                                     -    high-throughput sequencing data using a simple Bayesian network, the
                                     -    structure and parameters of which are trained on a set of aligned reads
                                     -    and a reference genome sequence.
                                     +Title: Estimation of per-position bias in high-throughput sequencing
                                     +        data
                                     +Description: This package implements a model of per-position sequencing
                                     +        bias in high-throughput sequencing data using a simple Bayesian
                                     +        network, the structure and parameters of which are trained on a
                                     +        set of aligned reads and a reference genome sequence.
                                      Author: Daniel Jones <dcjones@cs.washington.edu>
                                      Maintainer: Daniel Jones <dcjones@cs.washington.edu>
                                     -Depends: R (>= 2.13.0), GenomicRanges (>= 0.1.0),
                                     -         Biostrings (>= 2.15.0), methods
                                     +Depends: R (>= 2.13.0), GenomicRanges (>= 0.1.0), Biostrings (>=
                                     +        2.15.0), methods
                                      LinkingTo: Rsamtools
                                      Imports: zlibbioc
                                     -Suggests: Rsamtools, ggplot2
                                     -biocViews: Sequencing, HighThroughputSequencing
                                     +Suggests: Rsamtools, ggplot2
                                      LazyLoad: yes
                                      License: LGPL-3
+                                    -
                                     +biocViews: Sequencing, Sequencing

Browse code

rename inst/doc to vignettes and bump version

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@82629 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 01/11/2013 20:16:41
Showing 1 changed files

DESCRIPTION

History View file @ f8f3b4b

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.11.0
                                     +Version: 1.11.1
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

bump version after release branch has been created

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@81644 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 14/10/2013 21:47:19
Showing 1 changed files

DESCRIPTION

History View file @ d0f5dc3

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.10.0
                                     +Version: 1.11.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

bump versions prior to creating BioC 2.13 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@81642 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 14/10/2013 21:29:21
Showing 1 changed files

DESCRIPTION

History View file @ e467555

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.9.0
                                     +Version: 1.10.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

Bump y in version x.y.z to odd number in devel

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@75270 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/04/2013 22:06:11
Showing 1 changed files

DESCRIPTION

History View file @ eba47fa

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.8.0
                                     +Version: 1.9.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

bump y of x.y.z version number for BioC 2.12 release

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@75263 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/04/2013 21:32:27
Showing 1 changed files

DESCRIPTION

History View file @ 671ee49

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.7.0
                                     +Version: 1.8.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

bump package versions after creating 2.11 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@70052 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 01/10/2012 22:43:56
Showing 1 changed files

DESCRIPTION

History View file @ a893803

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.6.0
                                     +Version: 1.7.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

Bump all packages before creating 2.11 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@70050 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 01/10/2012 22:16:24
Showing 1 changed files

DESCRIPTION

History View file @ 4e0daeb

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.5.0
                                     +Version: 1.6.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

bumped version numbers after creating 2.10 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@64680 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 30/03/2012 22:15:56
Showing 1 changed files

DESCRIPTION

History View file @ 26640b4

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.4.0
                                     +Version: 1.5.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

first version bump prior to creating 2.10 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@64678 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 30/03/2012 22:05:02
Showing 1 changed files

DESCRIPTION

History View file @ 301bfce

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.3.1
                                     +Version: 1.4.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

Added Rsamtools and ggplot2 to Suggests

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@63624 bc3139a8-67e5-0310-9ffc-ced21a209358

Valerie Obenchain authored on 08/03/2012 21:13:37
Showing 1 changed files

DESCRIPTION

History View file @ 15b43f6

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.3.0
                                     +Version: 1.3.1
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in
@@ -12,6 +12,7 @@ Depends: R (>= 2.13.0), GenomicRanges (>= 0.1.0),
                                               Biostrings (>= 2.15.0), methods
                                      LinkingTo: Rsamtools
                                      Imports: zlibbioc
                                     +Suggests: Rsamtools, ggplot2
                                      biocViews: Sequencing, HighThroughputSequencing
                                      LazyLoad: yes
                                      License: LGPL-3

Browse code

version bump for start of 2.10 development cycle

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@59924 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 31/10/2011 23:12:28
Showing 1 changed files

DESCRIPTION

History View file @ baae205

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.2.0
                                     +Version: 1.3.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

bumped package version numbers prior to creating 2.9 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@59920 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 31/10/2011 22:59:03
Showing 1 changed files

DESCRIPTION

History View file @ 016c127

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.1.4
                                     +Version: 1.2.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

fix a check warning and a windows build error

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@59179 bc3139a8-67e5-0310-9ffc-ced21a209358

Daniel Jones authored on 13/10/2011 18:02:34
Showing 1 changed files

DESCRIPTION

History View file @ 30e3451

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.1.3
                                     +Version: 1.1.4
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in
@@ -11,6 +11,7 @@ Maintainer: Daniel Jones <dcjones@cs.washington.edu>
                                      Depends: R (>= 2.13.0), GenomicRanges (>= 0.1.0),
                                               Biostrings (>= 2.15.0), methods
                                      LinkingTo: Rsamtools
                                     +Imports: zlibbioc
                                      biocViews: Sequencing, HighThroughputSequencing
                                      LazyLoad: yes
                                      License: LGPL-3

Browse code

some small api improvements and cross-platform fixes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@59091 bc3139a8-67e5-0310-9ffc-ced21a209358

Daniel Jones authored on 11/10/2011 21:38:58
Showing 1 changed files

DESCRIPTION

History View file @ 9120a04

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.1.1
                                     +Version: 1.1.3
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

A complete refactor/rewrite of the original seqbias code. This should behave more or less identically, but is much more coherent.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@57223 bc3139a8-67e5-0310-9ffc-ced21a209358

Daniel Jones authored on 04/08/2011 07:36:48
Showing 1 changed files

DESCRIPTION

History View file @ 23b1bf8

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.1.0
                                     +Version: 1.1.1
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

Bumped version numbers again for new BioC 2.9 devel cycle.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@54802 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/04/2011 22:36:43
Showing 1 changed files

DESCRIPTION

History View file @ aee21de

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 1.0.0
                                     +Version: 1.1.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

Bumped version numbers for BioC 2.8 release.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@54800 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/04/2011 22:27:35
Showing 1 changed files

DESCRIPTION

History View file @ 38415b0

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 0.99.11
                                     +Version: 1.0.0
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

fix a random crash, a 64bit compile error, objects not getting properly cleaned, etc

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@54558 bc3139a8-67e5-0310-9ffc-ced21a209358

Daniel Jones authored on 06/04/2011 20:08:03
Showing 1 changed files

DESCRIPTION

History View file @ a864aa8

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 0.99.10
                                     +Version: 0.99.11
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

missing include

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@54149 bc3139a8-67e5-0310-9ffc-ced21a209358

Daniel Jones authored on 29/03/2011 20:06:53
Showing 1 changed files

DESCRIPTION

History View file @ 7d2e61d

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 0.99.9
                                     +Version: 0.99.10
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

fix a randomly occuring crash

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@54119 bc3139a8-67e5-0310-9ffc-ced21a209358

Daniel Jones authored on 28/03/2011 21:08:28
Showing 1 changed files

DESCRIPTION

History View file @ 989bb0a

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 0.99.8
                                     +Version: 0.99.9
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

updated to build against Rsamtools 1.3.29

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@54033 bc3139a8-67e5-0310-9ffc-ced21a209358

Daniel Jones authored on 25/03/2011 05:34:07
Showing 1 changed files

DESCRIPTION

History View file @ 93f8876

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 0.99.7
                                     +Version: 0.99.8
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

merged a number of improvements

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@53976 bc3139a8-67e5-0310-9ffc-ced21a209358

Daniel Jones authored on 23/03/2011 19:03:43
Showing 1 changed files

DESCRIPTION

History View file @ 0bd9720

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 0.99.6
                                     +Version: 0.99.7
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

remove repackaged samtools, link to Rsamtools

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@53961 bc3139a8-67e5-0310-9ffc-ced21a209358

Daniel Jones authored on 23/03/2011 07:12:04
Showing 1 changed files

DESCRIPTION

History View file @ ff7270e

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 0.99.5
                                     +Version: 0.99.6
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in
@@ -10,7 +10,7 @@ Author: Daniel Jones <dcjones@cs.washington.edu>
                                      Maintainer: Daniel Jones <dcjones@cs.washington.edu>
                                      Depends: R (>= 2.13.0), GenomicRanges (>= 0.1.0),
                                               Biostrings (>= 2.15.0), methods
                                     -Suggests: Rsamtools (>= 1.3.18)
                                     +LinkingTo: Rsamtools
                                      biocViews: Sequencing, HighThroughputSequencing
                                      LazyLoad: yes
                                      License: LGPL-3

Browse code

fix mingw compile errors

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@52629 bc3139a8-67e5-0310-9ffc-ced21a209358

Daniel Jones authored on 12/02/2011 03:53:41
Showing 1 changed files

DESCRIPTION

History View file @ bfa9f72

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 0.99.4
                                     +Version: 0.99.5
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

portability fixes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@52495 bc3139a8-67e5-0310-9ffc-ced21a209358

Daniel Jones authored on 06/02/2011 02:53:32
Showing 1 changed files

DESCRIPTION

History View file @ 24e9f1d

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 0.99.3
                                     +Version: 0.99.4
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

fixes for several compiler warnings and errors

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@52365 bc3139a8-67e5-0310-9ffc-ced21a209358

Daniel Jones authored on 02/02/2011 20:08:21
Showing 1 changed files

DESCRIPTION

History View file @ 0e7f1a0

@@ -1,5 +1,5 @@
                                      Package: seqbias
                                     -Version: 0.99.2
                                     +Version: 0.99.3
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                      Description: This package implements a model of per-position sequencing bias in

Browse code

Removed non-portable code. Minor algorithmic improvements.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@52193 bc3139a8-67e5-0310-9ffc-ced21a209358

Daniel Jones authored on 30/01/2011 05:41:26
Showing 1 changed files

DESCRIPTION

History View file @ 576e3e3

@@ -1,13 +1,13 @@
                                      Package: seqbias
                                     -Version: 0.99.1
                                     +Version: 0.99.2
                                      Date: 25-12-2010
                                      Title: Estimation of per-position bias in high-throughput sequencing data
                                     -Description: This package implements a model of per-position sequencing bias i
                                     +Description: This package implements a model of per-position sequencing bias in
                                          high-throughput sequencing data using a simple Bayesian network, the
                                          structure and parameters of which are trained on a set of aligned reads
                                          and a reference genome sequence.
                                      Author: Daniel Jones <dcjones@cs.washington.edu>
                                     -Maintainer: Dainel Jones <dcjones@cs.washington.edu>
                                     +Maintainer: Daniel Jones <dcjones@cs.washington.edu>
                                      Depends: R (>= 2.13.0), GenomicRanges (>= 0.1.0),
                                               Biostrings (>= 2.15.0), methods
                                      Suggests: Rsamtools (>= 1.3.18)

Browse code

Added the seqbias package to the repository.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@52013 bc3139a8-67e5-0310-9ffc-ced21a209358

Chao-Jen Wong authored on 22/01/2011 00:26:36
Showing 1 changed files

DESCRIPTION

History View file @ d958d35

                                     new file mode 100644
@@ -0,0 +1,17 @@
                                     +Package: seqbias
                                     +Version: 0.99.1
                                     +Date: 25-12-2010
                                     +Title: Estimation of per-position bias in high-throughput sequencing data
                                     +Description: This package implements a model of per-position sequencing bias i
                                     +    high-throughput sequencing data using a simple Bayesian network, the
                                     +    structure and parameters of which are trained on a set of aligned reads
                                     +    and a reference genome sequence.
                                     +Author: Daniel Jones <dcjones@cs.washington.edu>
                                     +Maintainer: Dainel Jones <dcjones@cs.washington.edu>
                                     +Depends: R (>= 2.13.0), GenomicRanges (>= 0.1.0),
                                     +         Biostrings (>= 2.15.0), methods
                                     +Suggests: Rsamtools (>= 1.3.18)
                                     +biocViews: Sequencing, HighThroughputSequencing
                                     +LazyLoad: yes
                                     +License: LGPL-3
+                                    +