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r
r
 
 
.gitignore
.gitignore
 
 
README.md
README.md
 
 
annotation_pie.py
annotation_pie.py
 
 
annotation_pie_gff.py
annotation_pie_gff.py
 
 
array_cors.py
array_cors.py
 
 
attach_nh.py
attach_nh.py
 
 
bam_12.py
bam_12.py
 
 
bam_bedg.py
bam_bedg.py
 
 
bam_combine_fragments.py
bam_combine_fragments.py
 
 
bam_fragments.py
bam_fragments.py
 
 
bam_heat.py
bam_heat.py
 
 
bam_len_hist.py
bam_len_hist.py
 
 
bam_plus_minus.py
bam_plus_minus.py
 
 
bam_quality.py
bam_quality.py
 
 
bam_unique.py
bam_unique.py
 
 
bed2fa.py
bed2fa.py
 
 
bed2gff.py
bed2gff.py
 
 
bed2gtf.py
bed2gtf.py
 
 
bed_clean.py
bed_clean.py
 
 
bedtools.py
bedtools.py
 
 
bg_w5.py
bg_w5.py
 
 
bgo_w5.py
bgo_w5.py
 
 
bim_vcf.py
bim_vcf.py
 
 
bl2gff.py
bl2gff.py
 
 
blastme.py
blastme.py
 
 
bw_nan.py
bw_nan.py
 
 
bw_w5.py
bw_w5.py
 
 
chain_map.py
chain_map.py
 
 
citemelike.py
citemelike.py
 
 
clean_csv.py
clean_csv.py
 
 
clean_gtf.py
clean_gtf.py
 
 
clean_merged_gtf.py
clean_merged_gtf.py
 
 
clear_slurm.py
clear_slurm.py
 
 
col2rows
col2rows
 
 
conservation_intersect.py
conservation_intersect.py
 
 
conservation_intersect_motif.py
conservation_intersect_motif.py
 
 
contrafold_viz.sh
contrafold_viz.sh
 
 
cors_gsea.py
cors_gsea.py
 
 
cors_gsea_setshuf.py
cors_gsea_setshuf.py
 
 
cuff_2d.py
cuff_2d.py
 
 
cuff_bar.py
cuff_bar.py
 
 
cuff_fails.py
cuff_fails.py
 
 
cuff_heat.py
cuff_heat.py
 
 
cuff_rep_cor.py
cuff_rep_cor.py
 
 
cuff_scatter.py
cuff_scatter.py
 
 
cuffdiff.py
cuffdiff.py
 
 
cuffify_gtf.py
cuffify_gtf.py
 
 
cufflinks.py
cufflinks.py
 
 
cutFasta.py
cutFasta.py
 
 
dexseq_prepare_annotation.py
dexseq_prepare_annotation.py
 
 
diff_diff.py
diff_diff.py
 
 
dna.py
dna.py
 
 
explore.ipynb
explore.ipynb
 
 
fasta_genome.py
fasta_genome.py
 
 
fasta_upper.py
fasta_upper.py
 
 
fastq_filter.py
fastq_filter.py
 
 
fastq_quality_change.py
fastq_quality_change.py
 
 
fastq_sample.py
fastq_sample.py
 
 
fastq_trim.py
fastq_trim.py
 
 
fdr.py
fdr.py
 
 
fimo_vcf.py
fimo_vcf.py
 
 
fire_map.py
fire_map.py
 
 
fpkm_fpkm.py
fpkm_fpkm.py
 
 
fpkm_hist.py
fpkm_hist.py
 
 
fpkm_tracking.py
fpkm_tracking.py
 
 
gaps_bed.py
gaps_bed.py
 
 
geneid2transid.py
geneid2transid.py
 
 
gff.py
gff.py
 
 
gff2bed.py
gff2bed.py
 
 
gff2fa.py
gff2fa.py
 
 
ggplot.py
ggplot.py
 
 
gsea.py
gsea.py
 
 
gsea_ranks.py
gsea_ranks.py
 
 
gsea_rnk.py
gsea_rnk.py
 
 
gtf2bed.py
gtf2bed.py
 
 
gtf2prom.py
gtf2prom.py
 
 
gtf2prom_bad.py
gtf2prom_bad.py
 
 
gtf2utrs.py
gtf2utrs.py
 
 
gtf_add_introns.py
gtf_add_introns.py
 
 
gtf_add_prerna.py
gtf_add_prerna.py
 
 
gtf_cut.py
gtf_cut.py
 
 
gtf_filter_csf.py
gtf_filter_csf.py
 
 
gtf_filter_expr.py
gtf_filter_expr.py
 
 
gtf_homologues.py
gtf_homologues.py
 
 
gtf_multimaps.py
gtf_multimaps.py
 
 
gtf_span.py
gtf_span.py
 
 
h5_h5z.py
h5_h5z.py
 
 
h5_sum.py
h5_sum.py
 
 
h5_zarr.py
h5_zarr.py
 
 
isoforms_fpkm.py
isoforms_fpkm.py
 
 
limit_duplicates.py
limit_duplicates.py
 
 
lnc_expression.py
lnc_expression.py
 
 
lnc_phylop.py
lnc_phylop.py
 
 
make_fasta_genome.py
make_fasta_genome.py
 
 
make_ref_ml.py
make_ref_ml.py
 
 
map_kmer.py
map_kmer.py
 
 
meme2possum.py
meme2possum.py
 
 
merge_gff_spliced.py
merge_gff_spliced.py
 
 
mess2fasta.py
mess2fasta.py
 
 

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utility

Computational biology utility scripts

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Computational biology utility scripts

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