1. MotifDb
  2. NAMESPACE
Browse code

removed motifmatchr and its dependencies

paul-shannon authored on 02/04/2020 20:20:03
Showing 1 changed files
NAMESPACE
History View file @ a3aca6d
... ... 
@@ -4,7 +4,6 @@ exportMethods (
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    export,
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    show,
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    query,
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-   matchMotif,
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    motifToGene,
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    geneToMotif,
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    associateTranscriptionFactors
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@@ -14,11 +13,6 @@ export(
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     MotifDb
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 )
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-import(motifmatchr)
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-import(TFBSTools)
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-importFrom(universalmotif, convert_motifs)
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-
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-
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 import(BiocGenerics)
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 import(S4Vectors)
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 import(IRanges)
Browse code

provisional addition of hocomoco v1, with reliability scores, A-D

paul-shannon authored on 10/03/2020 00:06:57
Showing 1 changed files
NAMESPACE
History View file @ 5b88116
... ... 
@@ -4,6 +4,7 @@ exportMethods (
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    export,
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    show,
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    query,
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+   matchMotif,
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    motifToGene,
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    geneToMotif,
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    associateTranscriptionFactors
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@@ -13,9 +14,15 @@ export(
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     MotifDb
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 )
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+import(motifmatchr)
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+import(TFBSTools)
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+importFrom(universalmotif, convert_motifs)
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+
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+
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 import(BiocGenerics)
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 import(S4Vectors)
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 import(IRanges)
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+import(GenomicRanges)
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 importFrom(rtracklayer, export)
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 import(Biostrings)
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 import(methods)
Browse code

motifToGene refactored, now suuports c('motifDb', tfClass') sources

paul-shannon authored on 18/05/2018 22:05:19
Showing 1 changed files
NAMESPACE
History View file @ aaf4e1a
... ... 
@@ -4,7 +4,6 @@ exportMethods (
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    export,
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    show,
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    query,
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-   query2,
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    motifToGene,
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    geneToMotif,
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    associateTranscriptionFactors
Browse code

added query2(mdb, andTerms, orTerms=c(), notTerms=c())

paul-shannon authored on 10/05/2018 23:52:12
Showing 1 changed files
NAMESPACE
History View file @ 3cb31fd
... ... 
@@ -4,6 +4,7 @@ exportMethods (
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    export,
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    show,
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    query,
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+   query2,
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    motifToGene,
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    geneToMotif,
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    associateTranscriptionFactors
Browse code

Removed large text files

Matthew Richards authored on 03/10/2017 16:42:17
Showing 1 changed files
NAMESPACE
History View file @ b7fe234
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@@ -20,3 +20,4 @@ importFrom(rtracklayer, export)
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 import(Biostrings)
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 import(methods)
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 importFrom(splitstackshape, expandRows)
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+importFrom(utils, read.table)
Browse code

geneToMotif, motifToGene, associateTranscriptionFactors tested

paul-shannon authored on 07/09/2017 23:28:23
Showing 1 changed files
NAMESPACE
History View file @ 49ebd9d
... ... 
@@ -4,8 +4,9 @@ exportMethods (
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    export,
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    show,
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    query,
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-   mapMotifToTranscriptionFactorGeneSymbol,
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-   mapTranscriptionFactorGeneSymbolToMotif
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+   motifToGene,
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+   geneToMotif,
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+   associateTranscriptionFactors
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    )
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 export(
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@@ -18,3 +19,4 @@ import(IRanges)
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 importFrom(rtracklayer, export)
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 import(Biostrings)
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 import(methods)
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+importFrom(splitstackshape, expandRows)
Browse code

roughed in data, methods and tests for mapping tf genes <--> motifs

paul-shannon authored on 13/08/2017 00:19:12
Showing 1 changed files
NAMESPACE
History View file @ 2def1ee
... ... 
@@ -3,7 +3,9 @@ exportMethods (
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    subset,
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    export,
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    show,
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-   query
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+   query,
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+   mapMotifToTranscriptionFactorGeneSymbol,
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+   mapTranscriptionFactorGeneSymbolToMotif
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    )
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 export(
Browse code

NAMESPACE now imports Biosrings and methods MotIV's need go gnu scientific library ("libgsl") prevents use of MotIV in the vignette.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@107860 bc3139a8-67e5-0310-9ffc-ced21a209358

p.shannon authored on 28/08/2015 04:58:55
Showing 1 changed files
NAMESPACE
History View file @ 10f8424
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@@ -14,4 +14,5 @@ import(BiocGenerics)
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 import(S4Vectors)
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 import(IRanges)
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 importFrom(rtracklayer, export)
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-
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+import(Biostrings)
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+import(methods)
Browse code

resync with latest changes in IRanges/S4Vectors

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@94017 bc3139a8-67e5-0310-9ffc-ced21a209358

hpages@fhcrc.org authored on 11/09/2014 00:33:01
Showing 1 changed files
NAMESPACE
History View file @ 64c5326
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@@ -10,7 +10,8 @@ export(
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     MotifDb
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 )
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-importMethodsFrom(IRanges, rbind, eval, sapply, subset, values)
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-importFrom(IRanges, DataFrame)
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+import(BiocGenerics)
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+import(S4Vectors)
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+import(IRanges)
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 importFrom(rtracklayer, export)
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Browse code

Adds PADOG, RMassBank, ChIPXpress, MotifDb, and GeneNetworkBuilder to the repos.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@68872 bc3139a8-67e5-0310-9ffc-ced21a209358

m.carlson authored on 28/08/2012 17:36:36
Showing 1 changed files
NAMESPACE
History View file @ b70c1a6
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new file mode 100644
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@@ -0,0 +1,16 @@
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+exportClasses (MotifList)
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+exportMethods (
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+   subset,
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+   export,
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+   show,
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+   query
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+   )
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+
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+export(
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+    MotifDb
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+)
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+
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+importMethodsFrom(IRanges, rbind, eval, sapply, subset, values)
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+importFrom(IRanges, DataFrame)
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+importFrom(rtracklayer, export)
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+