October 4, 2017

documentation for geneToMotif, motifToGene, associateT...

paul-shannon authored on 04/10/2017 19:49:25

lexical only: renamed 2 variables

paul-shannon authored on 04/10/2017 17:49:04
October 3, 2017

motifToGene sidesteps regexes by grep fixed=TRUE

paul-shannon authored on 03/10/2017 18:13:41
September 26, 2017

motif/TF mapping sources now case insensitive

paul-shannon authored on 26/09/2017 20:09:39
September 18, 2017

Fixed jaspar format spacing and updated DESCRIPTION

Matthew Richards authored on 18/09/2017 18:31:33
September 12, 2017

now annotates to TFs properly for MotifDb and TFClass sources

paul-shannon authored on 12/09/2017 20:20:46
September 7, 2017

geneToMotif, motifToGene, associateTranscriptionFactors tested

paul-shannon authored on 07/09/2017 23:28:23
August 13, 2017

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

paul-shannon authored on 13/08/2017 00:19:12
August 1, 2017

Updated unit tests to accomodate added motifs

Matthew Richards authored on 01/08/2017 16:44:49

Fixed 2 of 6 failing unit tests

Matthew Richards authored on 01/08/2017 00:26:44
June 15, 2017

Added jaspar output format and unit tests

Matthew Richards authored on 15/06/2017 22:50:54
August 28, 2015

in test.geneIdsAndTypes, typeCounts are now checked against minima, rather than absolute counts, hopting to make these tests robust against future additions to the data

p.shannon authored on 28/08/2015 20:43:22

expanded to top=50 rtahern top=5 in call to motifMatch, to ensure the search target is returned. this accomodates the peculiar fact MotIV's match algorithm and results differs on linux and macos

p.shannon authored on 28/08/2015 20:40:02

relaxed test.run_MotIV.motifMatch() success criteria so that the motif-to-match now needs only to be within the top 5 hits returned. it will not necessarily (by MotIV matching strategy) necessarily be the best match.

p.shannon authored on 28/08/2015 15:41:11

disabled references to MotIV: the .so for that (separate) package failed to install commented out call to tomtom: that is not routinely available corrected a number of tests for the newly added cisbp database

p.shannon authored on 28/08/2015 04:30:26