1. MotifDb
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bumped version to catch new knitr vignette, updated NEWS

paul-shannon authored on 14/04/2020 16:58:57
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NEWS
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+CHANGES IN VERSION 1.30
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+-----------------------
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+NEW FEATURES
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+
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+     o now has HOCOMOCO version 11, with all motifs classified, and queryable,
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+       by category ("core", "secondary") and reliability (A, B, C, D).
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+
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 CHANGES IN VERSION 1.24
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Browse code

improved docs for query method

paul-shannon authored on 24/10/2018 19:02:56
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NEWS
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+CHANGES IN VERSION 1.24
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+-----------------------
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+NEW FEATURES
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+     o query method now flexible, with "andStrings", "orStrings", "notStrings" parameters
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+       The previous usage style is still supported.  See man page.
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+
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+     o associateTranscriptionFactors (with motifs) substantially faster
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+
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 CHANGES IN VERSION 1.20
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Browse code

updated for release

paul-shannon authored on 13/10/2017 16:41:24
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NEWS
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+CHANGES IN VERSION 1.20
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+-----------------------
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+
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+NEW FEATURES
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+     o Now 13 sources, 52 organisms and 8369 motifs
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+
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+     o New sources: HOCOMOCOv10, HOMER, jaspar2016, SwissRegulon
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+
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+     o New methods: motifToGene, geneToMotif, associateTranscriptionFactors
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+
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+SIGNIFICANT USER-VISIBLE CHANGES
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+
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+     o The new methods mentioned above provide both strict and permissive
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+       mapping from motifs to their cognate transcription factors, thus
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+       supporting reproducible regulatory network construction.
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+
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 NEW FEATURES
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-    o 683 new motifs derived from DGF (digital genome footprinting)
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+    o 683 new motifs derived from DGF (digital genome footprinting)
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       from the stamlab (http://www.stamlab.org/) added.  Each is
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       identified as either 'knownMotif' or 'novelMotif'
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Browse code

added news about JASPAR_2014

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@88741 bc3139a8-67e5-0310-9ffc-ced21a209358

p.shannon authored on 10/04/2014 17:27:20
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NEWS
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+CHANGES IN VERSION 1.5.9
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+-------------------------
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+NEW FEATURES
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+    o JASPAR_2014 added, with 592 motifs
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 CHANGES IN VERSION 1.1.3
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Browse code

added novel/known annotation to the stamlab ratios, in the geneId metadata field

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@70918 bc3139a8-67e5-0310-9ffc-ced21a209358

p.shannon authored on 02/11/2012 03:38:12
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NEWS
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-CHANGES IN VERSION 1.1.2
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+CHANGES IN VERSION 1.1.3
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 NEW FEATURES
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     o 683 new motifs derived from DGF (digital genome footprinting)
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-      from the stamlab (http://www.stamlab.org/) added.
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+      from the stamlab (http://www.stamlab.org/) added.  Each is
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+      identified as either 'knownMotif' or 'novelMotif'
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+
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+
Browse code

added DGF motifs from the stamlab

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@70836 bc3139a8-67e5-0310-9ffc-ced21a209358

p.shannon authored on 30/10/2012 03:57:35
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NEWS
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new file mode 100644
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+CHANGES IN VERSION 1.1.2
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+-------------------------
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+
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+NEW FEATURES
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+
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+    o 683 new motifs derived from DGF (digital genome footprinting)
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+      from the stamlab (http://www.stamlab.org/) added.