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ae-merge-files.py

ae-merge-files.py

 
 

ae-quantify-from-bam.py

ae-quantify-from-bam.py

 
 

ae-quantify-from-junctions.py

ae-quantify-from-junctions.py

 
 

alt-splice-quantification.py

alt-splice-quantification.py

 
 

alt-splice-quantification.rev1.py

alt-splice-quantification.rev1.py

 
 

alt-splice-quantification.rev2.py

alt-splice-quantification.rev2.py

 
 

annot-peaks.py

annot-peaks.py

 
 

annotate-juncs.py

annotate-juncs.py

 
 

annotate-kallisto-pseudo.py

annotate-kallisto-pseudo.py

 
 

asi-build-index.py

asi-build-index.py

 
 

asi-build-index2.py

asi-build-index2.py

 
 

asi-build-indexG.py

asi-build-indexG.py

 
 

asi-count-from-junctions.py

asi-count-from-junctions.py

 
 

asi-indexG-quant-from-junctions.py

asi-indexG-quant-from-junctions.py

 
 

asi-indexG-quant.py

asi-indexG-quant.py

 
 

asi-miso-index-from-indexG.py

asi-miso-index-from-indexG.py

 
 

asi-reformat.py

asi-reformat.py

 
 

asplice-count-hits-intron.py

asplice-count-hits-intron.py

 
 

asplice-count-hits.py

asplice-count-hits.py

 
 

asplice-merge-files.py

asplice-merge-files.py

 
 

asplice-merge-intron-files.py

asplice-merge-intron-files.py

 
 

asplice-prepare-intron-reference.py

asplice-prepare-intron-reference.py

 
 

asplice-prepare-reference-beta2.py

asplice-prepare-reference-beta2.py

 
 

asplice-prepare-reference.py

asplice-prepare-reference.py

 
 

assem-report.py

assem-report.py

 
 

audit-R-code.py

audit-R-code.py

 
 

bam-bwa-split-filter.py

bam-bwa-split-filter.py

 
 

bam-filter-pe-unmapped.py

bam-filter-pe-unmapped.py

 
 

bam-filter.py

bam-filter.py

 
 

bam-galign-to-talign-fast.py

bam-galign-to-talign-fast.py

 
 

bam-gcounts-cs.py

bam-gcounts-cs.py

 
 

bam-gcounts-dev.py

bam-gcounts-dev.py

 
 

bam-gcounts-dev2.py

bam-gcounts-dev2.py

 
 

bam-gcounts-dev3-sp.py

bam-gcounts-dev3-sp.py

 
 

bam-gcounts-dev3.py

bam-gcounts-dev3.py

 
 

bam-gcounts-mp.py

bam-gcounts-mp.py

 
 

bam-gcounts-report.py

bam-gcounts-report.py

 
 

bam-gcounts.py

bam-gcounts.py

 
 

bam-genome-bin-counts.py

bam-genome-bin-counts.py

 
 

bam-genome-expr-quant.py

bam-genome-expr-quant.py

 
 

bam-index-template.py

bam-index-template.py

 
 

bam-stats.py

bam-stats.py

 
 

bam-to-fragment-bed.py

bam-to-fragment-bed.py

 
 

bam-to-junctions.py

bam-to-junctions.py

 
 

bam-to-tdf.py

bam-to-tdf.py

 
 

bam-vs-gtf.py

bam-vs-gtf.py

 
 

bam2fastq.py

bam2fastq.py

 
 

bam2juncsA.py

bam2juncsA.py

 
 

bamParse.py

bamParse.py

 
 

base-stats.py

base-stats.py

 
 

bootstrap.py

bootstrap.py

 
 

bowtie-express.py

bowtie-express.py

 
 

bowtie-mer-match.py

bowtie-mer-match.py

 
 

bstree.py

bstree.py

 
 

build-fastq-table.py

build-fastq-table.py

 
 

build-gtf.py

build-gtf.py

 
 

bwa-expandMulti-stream.py

bwa-expandMulti-stream.py

 
 

bwa-expandMulti.py

bwa-expandMulti.py

 
 

bwa-express.py

bwa-express.py

 
 

bwa-quant-sp.py

bwa-quant-sp.py

 
 

bwa-quant.py

bwa-quant.py

 
 

calc-kpseudo-quant.py

calc-kpseudo-quant.py

 
 

cluster-mappability-graph.py

cluster-mappability-graph.py

 
 

col-summary.py

col-summary.py

 
 

collapse-annotation.py

collapse-annotation.py

 
 

collapse.py

collapse.py

 
 

coverage-analysis.py

coverage-analysis.py

 
 

create-gene-shreds.py

create-gene-shreds.py

 
 

de_utils.py

de_utils.py

 
 

demux-10x-aligned.py

demux-10x-aligned.py

 
 

demux-10x-sorted.py

demux-10x-sorted.py

 
 

demux-cellranger-aligned.py

demux-cellranger-aligned.py

 
 

diff-exp.py

diff-exp.py

 
 

exactSnp-to-vcf.py

exactSnp-to-vcf.py

 
 

exon-useage-from-junctions.py

exon-useage-from-junctions.py

 
 

exon-useage.py

exon-useage.py

 
 

express-annotate-xprs.py

express-annotate-xprs.py

 
 

fa-orf-finder.py

fa-orf-finder.py

 
 

fasta-fix-filter.py

fasta-fix-filter.py

 
 

fasta-index.py

fasta-index.py

 
 

fasta-to-gtf.py

fasta-to-gtf.py

 
 

fasta-to-tab-delim.py

fasta-to-tab-delim.py

 
 

fasta2fastq.py

fasta2fastq.py

 
 

fastq-countReads.py

fastq-countReads.py

 
 

fastq-num-reads.py

fastq-num-reads.py

 
 

fastq-pairedSubset.py

fastq-pairedSubset.py

 
 

fastq-subset.py

fastq-subset.py

 
 

fastq2bam.py

fastq2bam.py

 
 

fastq2fasta.py

fastq2fasta.py

 
 

fft-signals.py

fft-signals.py

 
 

fixgid.py

fixgid.py

 
 

gene-cov-summary.py

gene-cov-summary.py

 
 

genomic.py

genomic.py

 
 

gtf-alternative-exons.py

gtf-alternative-exons.py

 
 

gtf-assembly-pipeline.py

gtf-assembly-pipeline.py

 
 

gtf-find-redundant.py

gtf-find-redundant.py

 
 

gtf-fixer.py

gtf-fixer.py

 
 

gtf-geneid-cluster.py

gtf-geneid-cluster.py

 
 

gtf-get-contained.py

gtf-get-contained.py

 
 

gtf-parse.py

gtf-parse.py

 
 

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All python all the time. This is a totally unorganized, straight copy of my own local python folder.

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