Junction Based Analysis of Splicing Events for RNA-Seq
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opus7 add opus7 Sep 23, 2014
other_scripts Create README Jan 20, 2017
MANUAL.pdf Added pdf manual Dec 9, 2015
adjust_KN_flag.py fixed jcn strings in adjust_KN_Flag.py Jan 22, 2013
buildVirtualReference_median.py Minor bug in buildVirtual Jul 26, 2012
build_DB_FromGTF.py Modified to only process 'exon' rows in a GTF file Mar 21, 2016
clusterASExons2.py clusterASExons2.py: resolving gene and strand information when there … Aug 6, 2012
combine_clusterASExons2_by_chr.py combine_clusterASExons2_by_chr.py: finished first build Jul 26, 2012
combine_createAS_CountTables_by_chr.py Fixed minor bugs Apr 25, 2013
compareJuncBASETables.py Tested new compare_pval option Oct 7, 2013
compareSampleSets.py Fixed error in option check Mar 6, 2014
compareSampleSets_getASEvents.py Ability to produce pdf images instead of png in compareSampleSets Jan 14, 2013
compareSampleSets_permutation.py Added function to deal with duplicate numbers in sets. Dec 17, 2013
compareSampleSets_permutation_kmeans.py Changed vgam function to rbetabinom_ab Dec 12, 2013
convert_junction_sam.py Added other_scripst into the directory Jan 18, 2013
coordReadCounts.py Added missing coordReadCounts.py Dec 9, 2015
coord_helperFunctions.py Bug in findOverlapCoords function. It was not calling itself Oct 3, 2013
createAS_CountTables.py Added more checks in creating the AS tables Apr 25, 2013
createPseudoSample.py Added an additional check when getting chr names Aug 10, 2012
disambiguate_junctions.py Small bug Apr 20, 2013
extractConfidentNNjunctions.py Added other_scripst into the directory Jan 18, 2013
fisherTest_exclusionInclusion.py Checked for header line in input Mar 25, 2014
getASEventReadCounts.py Fixed bugs in MXE and CCE Apr 27, 2013
getIntronRetentionEvents.py Wrong format of intron-exon junction coordinates Apr 2, 2013
getSimpleAS.py Added a script to extract only simpleAS events Dec 11, 2013
getSpecificSequences.py Added other_scripst into the directory Jan 18, 2013
helperFunctions.py Fixed queue problem Aug 1, 2013
intron_exon_jctn_counts.py Changed step3 for new coordinate string Dec 26, 2012
makeNonRedundantAS.py Optimized runs and fixed errors in finding nonRedundant events Aug 1, 2013
merge_by_chr_juncBASE_junction_file.py Error in including pseudo samples Aug 13, 2014
pairwise_fishers_test_getASEvents_w_reference.py Error in division of length with EXON_LEN Mar 30, 2013
plotEntropyScores.py Changed to matplotlib graphing Dec 3, 2012
preProcess_getASEventReadCounts.py Added check for odd junctions that are toward the beginning of a chro… Jan 29, 2014
preProcess_getASEventReadCounts_by_chr.py Added check for odd junctions that are toward the beginning of a chro… Jan 29, 2014
preProcess_getASEventReadCounts_by_chr_step2.py Fixed bug in import statement Dec 9, 2015
preProcess_getASEventReadCounts_step2.py Started converting the coordinate string to a format that allows for … Dec 22, 2012
preProcess_getASEventReadCounts_step3.py Removing unnecessary command line options Dec 24, 2012
pysqlite_wrap.py Updated to work with newer versions of pysqlite2 Dec 9, 2015
run_buildVirtualReference.py Finished run_buildVirtualReference Jan 23, 2013
run_build_DB_FromGTF_by_chr.py run_build_DB_FromGTF_by_chr.py: Minor bug in checkChr Aug 1, 2012
run_clusterASExons2_by_chr.py run_clusterASExons2_by_chr.py: Forgot to add counter to batch jobs Jul 27, 2012
run_createAS_CountTables.py Fixed directory of input files Feb 26, 2013
run_getASEventReadCounts_multiSample.py Samples will be taken from the first column of the input samples file May 13, 2014
run_preProcess_by_chr_step1.py Had to change the logic of checking for jobs to run Feb 13, 2013
run_preProcess_step3_by_chr.py Added --nice option to step3 Apr 22, 2013
sequence_wrap.py Included sequence_wrap module Mar 21, 2016