Unsorted scripts for bioinformatics

Miscellanea of scripts for bioinformatics. Many of these scripts do something very specific and they don't deserve their own repository. The quality of these programs can vary a lot, some are reasonably well designed and tested others are just stubs that started and I haven't finished.

Formerly was on google.code as bioinformatics-misc

Name		Name	Last commit message	Last commit date
Latest commit History 587 Commits
BSmatrix		BSmatrix
BaseSpaceDownloader		BaseSpaceDownloader
addContextToBed		addContextToBed
bam2methylation		bam2methylation
bedProfiler		bedProfiler
checkTerminatorBlock		checkTerminatorBlock
crossTabulate		crossTabulate
eclipse		eclipse
fastaFromBed		fastaFromBed
fastaRegexFinder		fastaRegexFinder
genomeFileFromBam		genomeFileFromBam
getBarcodeFromRNAseq		getBarcodeFromRNAseq
getUniqueLines		getUniqueLines
guidelines		guidelines
interleaveFastq		interleaveFastq
localEnrichmentBed		localEnrichmentBed
mergeBedLines		mergeBedLines
oxbs_qc		oxbs_qc
partitionBed		partitionBed
quickPlots		quickPlots
roslin		roslin
samChromUCSCtoNCBI		samChromUCSCtoNCBI
segmentPvalueByHMM		segmentPvalueByHMM
sortBedAsBam		sortBedAsBam
tableCat		tableCat
textHist		textHist
ucscTableToGTF		ucscTableToGTF
zzz_deprecated		zzz_deprecated
BSdata.R		BSdata.R
BSreshape.py		BSreshape.py
BaseSpaceAPI.R		BaseSpaceAPI.R
LSFbatchSubmit.py		LSFbatchSubmit.py
MbiasBismark.py		MbiasBismark.py
README.md		README.md
TPM.R		TPM.R
addAlignmentTagsToBam.py		addAlignmentTagsToBam.py
addCGcontextToBdg.sh		addCGcontextToBdg.sh
addRGtoSAMHeader.py		addRGtoSAMHeader.py
addSeqToFastqName.py		addSeqToFastqName.py
add_methylated_tag.py		add_methylated_tag.py
bam2grPrepareBam.py		bam2grPrepareBam.py
bam2methylation.py		bam2methylation.py
bam_read_length.py		bam_read_length.py
bamqc.py		bamqc.py
bamqc_batch_lustre.py		bamqc_batch_lustre.py
basename.py		basename.py
bedDist.R		bedDist.R
bed_windows.py		bed_windows.py
bedtools.R		bedtools.R
bismark2BSseq.py		bismark2BSseq.py
bismark_mapping_report2tab.py		bismark_mapping_report2tab.py
bismark_pipeline.py		bismark_pipeline.py
bsdata_glm.R		bsdata_glm.R
bsdata_glm2.R		bsdata_glm2.R
bwa_align.template.py		bwa_align.template.py
cat_mark_duplicates_stats.py		cat_mark_duplicates_stats.py
cleanBamReadNames.py		cleanBamReadNames.py
compressBedByWindows.py		compressBedByWindows.py
concatenate_ame.py		concatenate_ame.py
concatenate_bed.py		concatenate_bed.py
concatenate_files.py		concatenate_files.py
countBarcodesBam.py		countBarcodesBam.py
countFastqTags.py		countFastqTags.py
coverageBedRpkm.py		coverageBedRpkm.py
db001.test.fq.gz		db001.test.fq.gz
deconcatenate.py		deconcatenate.py
demux_fuzzy.py		demux_fuzzy.py
dexseq_coords.py		dexseq_coords.py
fastaRegexFinder.py		fastaRegexFinder.py
fastqSplitter.py		fastqSplitter.py
fastq_hist.py		fastq_hist.py
fastq_read_length.py		fastq_read_length.py
fastqc_data.txt		fastqc_data.txt
fastqc_md5.py		fastqc_md5.py
fastqc_to_pgtable.py		fastqc_to_pgtable.py
file2latexTable.py		file2latexTable.py
filterMethylatedReads.py		filterMethylatedReads.py
fimoToGlobalCoordsBed.py		fimoToGlobalCoordsBed.py
findEqualPairs.py		findEqualPairs.py
fixBam.py		fixBam.py
format_table.py		format_table.py
geneLengthFromGTF.py		geneLengthFromGTF.py
gene_profiler.py		gene_profiler.py
getReadsByName.py		getReadsByName.py
get_UTR_from_refGene.py		get_UTR_from_refGene.py
get_fastq_barcodes.py		get_fastq_barcodes.py
get_file_stats.py		get_file_stats.py
get_file_stats2.py		get_file_stats2.py
glm.R		glm.R
groupMetGraphByFeature.py		groupMetGraphByFeature.py
gtf2gene.py		gtf2gene.py
hexToRColour.R		hexToRColour.R
hmC_seeker.py		hmC_seeker.py
htseq_matrix.py		htseq_matrix.py
illumina2sanger.py		illumina2sanger.py
intensityFilter.R		intensityFilter.R
localEnrichmentBed.py		localEnrichmentBed.py
localEnrichmentScore.R		localEnrichmentScore.R
macs2ToNarrowPeak.py		macs2ToNarrowPeak.py
macsToNarrowPeak.py		macsToNarrowPeak.py

zzygyx9119/bioinformatics-cafe

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