Index of /kundaje/marinovg/oak/various/code/transcriptome

[ICO]NameLast modifiedSizeDescription
[PARENTDIR]Parent Directory  -  
[TXT]twintrons.py2013-03-04 18:02 3.8K 
[TXT]transcripts-vs-repeats.py2013-08-23 00:00 5.5K 
[TXT]transcripts-vs-repeats-enrichment.py2013-08-25 08:48 6.8K 
[TXT]transcriptome-make-reads.py2014-06-04 18:43 2.5K 
[TXT]transcriptome-make-reads-junctions.py2014-06-04 21:23 4.3K 
[TXT]tracking-stats.py2010-08-29 07:05 4.4K 
[TXT]tandemJunctionsMinimumHammingDistanceBetweenSpliceSites.py2012-03-18 09:17 7.8K 
[TXT]tandemJunctionsCorrelationWithExpression.py2012-03-17 13:12 4.1K 
[TXT]tandemJunctionsBioTypes.py2012-03-18 10:24 1.8K 
[TXT]sum.junctions.counts.py2010-07-20 07:06 937  
[TXT]stringtieMergeRename.py2017-06-13 16:11 5.0K 
[TXT]stalledTSSfromwig.py2011-11-15 22:41 5.2K 
[TXT]stalledPolII.py2011-03-02 17:44 29K 
[TXT]splicesfromgtf.py2010-07-20 03:07 2.0K 
[TXT]skippedExonsList.py2012-11-15 17:40 4.9K 
[TXT]skippedExonsInclusionScore.py2012-11-15 17:57 3.5K 
[TXT]singlemodelgenes.py2010-08-24 12:33 1.7K 
[TXT]singleExonTranscripts.py2012-03-11 14:55 2.3K 
[TXT]singleCellTypeSpecific.py2010-08-29 15:03 4.7K 
[DIR]simulations/2019-03-01 10:48 -  
[TXT]shuffle-annotation.py2013-08-23 01:08 4.5K 
[TXT]sequenceBiasPerExon.py2010-03-25 12:05 2.5K 
[TXT]sampleSAM.py2011-07-14 13:55 2.2K 
[TXT]retainedIntronsCleanUp.py2011-10-11 14:56 5.9K 
[TXT]renameCuffmergeTranscripts.py2011-10-15 01:41 6.1K 
[TXT]removePolyA.py2012-06-24 10:28 1.9K 
[TXT]removeDuplicatesFromGTF.py2011-09-11 09:57 4.6K 
[TXT]readsOnGenes.py2011-11-18 19:39 5.1K 
[TXT]pairedendlengthdistributionstatstable.py2011-06-08 10:37 1.1K 
[TXT]pairedendlengthdistributionstats.py2011-06-08 09:40 1.6K 
[TXT]pairedendlengthdistribution.py2012-03-14 19:36 5.0K 
[TXT]numExonsFromgtf-transcripts.py2010-08-11 12:32 1.8K 
[TXT]numExonsFromgtf-genes.py2011-12-30 06:29 1.9K 
[TXT]novelCufflinksTranscripts.py2010-11-16 18:40 2.2K 
[TXT]nomogram.py2013-04-14 20:40 3.5K 
[TXT]nearestKnownJunction2.py2013-02-05 11:49 3.1K 
[TXT]nearestKnownJunction.py2011-02-25 16:02 4.8K 
[TXT]multiExonTranscripts.py2012-10-09 20:06 2.3K 
[TXT]makewigglefromgtf.py2019-10-21 17:44 3.3K 
[TXT]make_FPKM_Wiggle_From_GTF.py2023-09-23 22:09 3.6K 
[TXT]makeTSSbedfromGENCODEgtf.py2010-09-01 04:38 1.9K 
[TXT]lincRNA.py2012-10-15 21:25 5.4K 
[DIR]leafcutter/2017-07-18 20:51 -  
[TXT]junctionsfromSAM.py2011-07-19 04:01 5.9K 
[TXT]junctionsfromGTF.py2011-02-05 13:10 2.0K 
[TXT]junctionsfromBAM.py2014-08-18 04:59 8.7K 
[TXT]junctionsTable.py2010-06-15 06:48 3.5K 
[TXT]junctionsPresenceAcrossReplicates.py2013-06-17 08:51 1.2K 
[TXT]juncsToBed.py2012-10-10 13:02 1.5K 
[TXT]indexsortmalesplices.sh2010-06-05 00:39 663  
[TXT]indexsortmale.sh2010-06-05 00:39 541  
[TXT]indexsortfemalesplices.sh2010-06-16 20:38 657  
[TXT]indexsortfemale.sh2010-06-04 17:58 534  
[TXT]gtf-to-transcripts-bed.py2022-12-14 18:06 2.5K 
[TXT]gtf-to-juncs.py2011-11-17 12:53 4.7K 
[TXT]gtf-to-fastaFromFasta.py2023-07-04 09:34 6.8K 
[TXT]gtf-to-fasta.py2013-03-02 09:24 4.2K 
[TXT]gtf-to-exons.py2018-02-03 14:35 1.7K 
[TXT]gff-to-juncs.py2010-12-23 08:25 1.9K 
[TXT]getSequenceAroundSplices.py2013-11-14 15:36 3.2K 
[TXT]getGTFTranscripts.py2012-10-16 23:01 1.1K 
[TXT]getGTFGenes.py2014-04-03 15:15 1.3K 
[TXT]gene_coverage_wig_gtf.py2017-06-06 16:03 5.6K 
[TXT]geneRPMfromBAM.py2011-08-29 19:58 4.8K 
[TXT]geneLengthsFromGTF.py2013-03-03 00:59 3.4K 
[TXT]flipwigsign.py2010-10-15 08:09 1.2K 
[TXT]fix_ENSEMBL_GTF.py2019-08-21 17:23 2.6K 
[TXT]fixWig.py2010-08-13 18:11 1.3K 
[TXT]fixTIF-seq-updated.py2021-01-03 08:21 5.1K 
[TXT]fixSAM.py2010-07-23 10:03 1.5K 
[TXT]first5pSpliceSite.py2012-11-30 15:18 3.8K 
[TXT]first3pSpliceSite.py2012-11-30 13:12 3.2K 
[TXT]filtercuffcomparetracking.py2010-03-21 12:33 3.0K 
[TXT]filterTracking.py2010-08-29 05:41 1.3K 
[TXT]filterSAMSplices.py2010-05-26 21:58 1.0K 
[TXT]filterNovel5ends.py2010-08-23 19:45 4.4K 
[TXT]filterGTFbyFPKM.py2011-10-07 20:03 1.6K 
[TXT]filterGTFbyClassCode.py2011-10-11 08:04 1.0K 
[TXT]fastq-SL-trim-and-append.py2021-02-03 07:35 3.4K 
[TXT]exonLengthDistribution.py2009-11-23 19:08 1.5K 
[TXT]exonFPKMfromCuflfinksGTF.py2012-05-06 23:37 2.6K 
[TXT]distinct_3-5-end_genes_from_gtf.py2011-06-23 17:58 4.1K 
[TXT]cufflinks-to-expression-table.py2011-03-01 06:15 5.2K 
[TXT]cufflinks-Novel-splices.py2010-03-21 10:33 2.7K 
[TXT]cuffdiffStats.py2011-07-29 07:18 5.7K 
[TXT]cuffdiffFilterGenes.py2011-11-24 20:39 3.8K 
[TXT]coverage_CV.py2013-07-22 17:17 9.0K 
[ ]commoncode.pyc2010-08-16 16:33 52K 
[TXT]commoncode.py2010-08-16 16:33 69K 
[TXT]commonFirstOrLastExons.py2011-10-31 13:34 3.3K 
[TXT]combineTSS-data-with-Constructs.py2011-10-04 15:12 1.8K 
[TXT]combineTSS-FPKM-table-with-TSSbed.py2011-10-04 13:28 1.4K 
[TXT]combinePhyloCSFresults.py2012-10-15 22:33 1.1K 
[TXT]combineJunctions.py2011-08-24 02:38 3.1K 
[TXT]combineExonConservationAndClassification.py2010-08-24 16:02 2.9K 
[TXT]circularRNAReadsToBackSplicesFasta.py2013-04-07 00:59 11K 
[TXT]circularRNAJunctions.py2013-04-03 09:52 4.3K 
[TXT]circularRNACombineBackSplicesWithRPM.py2013-04-07 23:22 6.0K 
[TXT]circularRNA.py2018-10-02 10:46 12K 
[TXT]circRNAExpression-vs-GeneExpression-combine.py2017-08-25 08:21 12K 
[TXT]chrMstats.py2010-06-10 15:12 2.7K 
[TXT]catalogueSplices.py2010-08-11 04:57 14K 
[TXT]catalogueJunctions.py2010-11-22 06:36 11K 
[TXT]catalogueExonsOfAnnottedGenes.py2011-10-31 13:13 11K 
[TXT]catalogueExons.py2010-07-28 23:56 7.3K 
[TXT]cannonicalJunctionsStrandGuess.py2011-03-17 09:31 3.9K 
[TXT]cannonicalJunctions.py2013-02-17 08:53 3.5K 
[TXT]biotypeGeneAndTranscriptIDs.py2018-11-21 10:04 2.5K 
[TXT]addStrandToJunctions.py2011-02-09 15:44 3.8K 
[TXT]addNamesTomRNAfafromRefKnown.py2012-02-25 15:44 1.3K 
[TXT]addNamesToGTFfromRefKnown.py2011-12-17 00:12 1.2K 
[TXT]addGeneNamesToGTF.py2013-04-29 20:35 1.3K 
[TXT]addAnnotationToCuffmergeOutput.py2011-10-13 23:39 5.8K 
[ ]add-xs.awk2010-06-04 06:41 756  
[TXT]ZeroBPTranscriptsGTF.py2011-10-10 21:58 1.3K 
[TXT]WatsonCrickSlidingWindow.py2009-07-22 18:58 3.2K 
[TXT]WatsonCrickGTF.py2010-03-22 09:07 4.2K 
[TXT]WatsonCrickExon.py2010-11-18 00:31 4.4K 
[TXT]WatsonCrickBed.py2010-11-18 12:23 2.5K 
[TXT]TranscribedFractionOfGenome.py2012-03-04 15:19 5.5K 
[TXT]TopHatJunctionsBedToJunctions.py2011-03-19 13:20 1.2K 
[TXT]TTS_bed_FromGTF-V2.py2019-09-12 14:55 4.8K 
[TXT]TSSsupport.py2011-10-06 20:08 6.8K 
[TXT]TSSexpression_from_Cufflinks.py2012-05-12 09:04 6.4K 
[TXT]TSSexpression-from-cufflinks[OLD].py2010-09-01 04:59 2.9K 
[TXT]TSScombineLCout.py2017-08-02 17:11 3.7K 
[TXT]TSS_bed_FromGTF.py2017-01-01 23:55 3.7K 
[TXT]TSS_bed_FromGTF-V2.py2022-03-28 07:10 5.3K 
[TXT]TSS_bed_FromGFF-genes.py2019-08-27 19:19 2.6K 
[TXT]TSSExtensionsORFImpact.py2012-03-27 18:01 3.1K 
[TXT]TSSCAGEreannotate.py2018-01-19 15:01 3.4K 
[TXT]TIF-seq-GTF-update.py2020-03-13 21:11 5.9K 
[TXT]Splicing35PsiScores.py2013-11-19 12:58 6.9K 
[TXT]SpliceUnsplicedReadsFromBAM.py2015-01-18 06:00 8.6K 
[TXT]STARcombineSJout.py2017-05-30 14:55 7.0K 
[TXT]SLmatches.py2021-02-03 07:24 4.3K 
[TXT]SAM_reads_in_genes4_BAM.py2017-06-06 19:59 6.0K 
[TXT]SAM_reads_in_genes3_BAM.py2017-06-06 19:15 6.2K 
[TXT]SAM_reads_in_genes2.py2011-10-22 11:05 6.4K 
[TXT]SAM_reads_in_genes.py2011-07-20 18:25 5.6K 
[TXT]SAMChromOrder.py2011-04-20 02:21 948  
[TXT]RPKMfraction.py2010-08-10 20:28 3.2K 
[DIR]RGASP/2011-01-29 07:35 -  
[TXT]RAMPAGE-clusters.py2017-06-23 23:23 15K 
[TXT]RAMPAGE-clusters-V2.py2025-06-03 20:20 17K 
[TXT]RAMPAGE-PAS-clusters-merge.py2017-08-02 22:45 6.3K 
[TXT]PSLtoGTF.py2022-12-09 14:06 3.8K 
[TXT]PAS-seq-clusters.py2017-06-23 23:23 16K 
[TXT]PAS-seq-clusters-V2.py2017-06-24 12:22 19K 
[TXT]OrthologyTableMGIMouseHuman.py2011-09-22 08:05 3.8K 
[TXT]ORFvariants.py2011-11-25 22:19 1.6K 
[TXT]ORFfromgtf2.py2012-10-15 13:14 8.2K 
[TXT]ORFfromgtf.py2011-12-23 19:34 8.0K 
[TXT]ORFGTF.py2012-09-28 20:30 1.1K 
[TXT]OK_status_isoform_pairs.py2011-10-07 18:29 3.2K 
[TXT]NumberIsoforms.py2011-12-23 19:01 1.4K 
[TXT]NumberExpressedTSS.py2012-03-11 09:48 3.8K 
[TXT]NovelSpliceJunctions.py2011-10-26 12:13 4.0K 
[TXT]Novel5ends.py2011-10-04 09:11 8.8K 
[TXT]Novel5ends-stats.py2010-08-23 20:49 2.1K 
[TXT]NMDannotationGTF.py2011-12-30 10:29 4.0K 
[TXT]MakeTranscriptomeFasta.py2011-06-24 22:22 11K 
[TXT]JunctionsFastaFromGTF.py2012-07-12 14:04 4.0K 
[TXT]IsoformSwitches.py2011-11-02 12:07 4.6K 
[TXT]IsoformStats2.py2011-03-03 15:26 8.8K 
[TXT]IsoformStats.py2010-10-31 17:16 5.9K 
[TXT]IsoformJunctionSupportFPKM.py2012-07-15 09:10 8.1K 
[TXT]IsoformJunctionSupport.py2012-01-09 15:04 6.8K 
[TXT]IsoformExprStatistics.py2011-11-22 14:23 5.4K 
[TXT]IntronLengthsPerPosition.py2017-06-16 00:03 4.3K 
[DIR]IDR/2010-12-16 08:44 -  
[TXT]GTFtoProteinFasta2.py2012-10-14 22:13 9.6K 
[TXT]GTFtoProteinFasta.py2012-10-14 21:53 10K 
[TXT]GTFtoAntiSenseGTF.py2014-12-10 23:44 2.1K 
[TXT]GTFsubset.py2011-09-01 21:00 1.1K 
[TXT]GTFstats.py2013-11-17 04:56 11K 
[TXT]GTFdupsrename.py2023-07-18 00:45 3.1K 
[TXT]GTFcomparisonV2-for-counting.py2022-12-12 15:58 9.9K 
[TXT]GTFcomparison---do-not-use.py2022-11-21 19:37 9.6K 
[TXT]GTFTranscriptSubset.py2022-12-12 16:25 1.5K 
[TXT]GTFRepeatMaskOverlap.py2014-04-03 15:42 4.3K 
[TXT]GTFGenesTranscriptsBioTypes.py2017-09-24 10:28 2.6K 
[TXT]GTF-to-ExonBed.py2014-11-24 15:58 3.3K 
[TXT]GFFToGTF.py2025-03-10 21:11 41K 
[TXT]GENCODEstats.py2011-12-30 11:04 3.1K 
[TXT]FluxGTFtoFPKM.py2014-09-15 09:11 1.4K 
[TXT]FMI_known_novel.py2012-07-13 19:25 5.8K 
[TXT]FMI-distribution.py2014-03-16 01:03 2.4K 
[TXT]ExonStatssummary.py2010-08-11 08:22 1.5K 
[TXT]ExonRepeatOverlapHyperGeometricTest.py2017-07-09 19:09 3.3K 
[TXT]ExonRepeatOverlap.py2017-07-10 18:05 6.6K 
[TXT]ExonPhasingFromGTF.py2013-06-01 18:00 2.6K 
[TXT]ExonIntronExonRPKMRatioPickGenes.py2013-03-15 08:39 1.5K 
[TXT]ExonIntronExonRPKMRatio.py2013-03-15 07:04 1.7K 
[TXT]ExonIntronExon.py2013-03-13 22:11 2.8K 
[TXT]ElementsStats.py2014-03-14 21:21 6.4K 
[TXT]ENSEMBLgeneIDs.py2011-11-05 00:23 1.3K 
[TXT]ENSEMBLE_IDs_to_GeneNames.py2011-02-06 04:46 2.0K 
[TXT]ENCODE-RPKM-from-GTF.py2014-06-11 07:45 2.1K 
[TXT]CDS-UTR-from-gtf.py2011-03-07 22:36 2.7K 
[TXT]CDS-UTR-from-gtf-V2.py2017-06-03 17:54 7.8K 
[TXT]BEDtoGTF.py2025-08-28 19:48 1.7K 
[TXT]2021-02-02-CAGE-RAMPAGE-processing-command-generate.py2021-02-03 02:59 22K 
[TXT]5-endstats.py2010-06-08 21:02 2.3K 
[TXT]5-3-RNA-Seq.py2011-01-13 19:18 7.8K 
[TXT]5-3-RNA-Seq-cumulative.py2011-03-04 08:10 2.8K 
[TXT]3ends.py2011-03-26 13:23 3.8K 
[TXT]3endGTF.py2025-08-13 01:43 8.1K 
[TXT]3ExonfromGTF.py2012-03-10 05:17 5.5K 
[TXT]2Dhistogram_for_junction_types.py2012-03-26 13:00 2.6K 
[TXT]2Dhistogram_for_junction_connectivity_types.py2011-10-26 14:44 1.8K 
[TXT]2Dhistogram_for_junction_connectivity.py2011-10-26 16:04 2.2K 
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