GitHub - mmarchin/utilities: A bunch of scripts for bioinformatic purposes

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 21 Commits
README		README
all2many.pl		all2many.pl
bam2sam.sh		bam2sam.sh
bedlengths.pl		bedlengths.pl
bedmid.pl		bedmid.pl
bedtss.pl		bedtss.pl
blat.sh		blat.sh
breakfasta.pl		breakfasta.pl
checkservers.sh		checkservers.sh
chromsizeswin.pl		chromsizeswin.pl
colMeans.pl		colMeans.pl
colgrep.sh		colgrep.sh
collapse.pl		collapse.pl
collapse.sh		collapse.sh
colors.pl		colors.pl
colors.sh		colors.sh
concatfasta.pl		concatfasta.pl
countbam.sh		countbam.sh
cutmulti.sh		cutmulti.sh
deriv.pl		deriv.pl
double.pl		double.pl
fakeid.pl		fakeid.pl
fasta2pwm.pl		fasta2pwm.pl
fastaheaders.pl		fastaheaders.pl
fastq2flat.pl		fastq2flat.pl
fetchChromSizes.sh		fetchChromSizes.sh
filterbed.pl		filterbed.pl
findzeros.pl		findzeros.pl
fix.pl		fix.pl
fixcols.pl		fixcols.pl
flatten.pl		flatten.pl
flatten2.pl		flatten2.pl
flatten_ragged.pl		flatten_ragged.pl
fpkm2bed.pl		fpkm2bed.pl
gal_check.pl		gal_check.pl
gcfiltfasta.pl		gcfiltfasta.pl
gen_logos.pl		gen_logos.pl
get_chroms.R		get_chroms.R
interlace.pl		interlace.pl
introns_from_gtf.pl		introns_from_gtf.pl
keeplongestbed.pl		keeplongestbed.pl
lenfiltfasta.pl		lenfiltfasta.pl
lines.pl		lines.pl
make60.pl		make60.pl
makefasta.pl		makefasta.pl
makerandom.pl		makerandom.pl
makewin.pl		makewin.pl
modcol.pl		modcol.pl
mysplitter.pl		mysplitter.pl
parseBlast.pl		parseBlast.pl
parseBlat.pl		parseBlat.pl
parseInParanoid.pl		parseInParanoid.pl
parse_bowtie2_err.pl		parse_bowtie2_err.pl
parse_bowtie2_paired_err.pl		parse_bowtie2_paired_err.pl
parse_bowtie_err.pl		parse_bowtie_err.pl
parse_fastx_clipper_err.pl		parse_fastx_clipper_err.pl
partfasta.pl		partfasta.pl
password.php		password.php
random_bed.pl		random_bed.pl
random_beds.sh		random_beds.sh
random_beds_dir.sh		random_beds_dir.sh
randomlines.pl		randomlines.pl
range.sh		range.sh
rearrange.pl		rearrange.pl
remove_NA.pl		remove_NA.pl
remove_overlaps.pl		remove_overlaps.pl
remove_roman.pl		remove_roman.pl
remove_scinums.pl		remove_scinums.pl
renamebed.pl		renamebed.pl
renamefasta.pl		renamefasta.pl
renamefasta2.pl		renamefasta2.pl
resize.sh		resize.sh
revcompfasta.pl		revcompfasta.pl
revfasta.pl		revfasta.pl
revfastq.pl		revfastq.pl
selectlines.pl		selectlines.pl
sparsewig.pl		sparsewig.pl
split_bed.pl		split_bed.pl
split_by_col.pl		split_by_col.pl
split_wig.pl		split_wig.pl
squish.pl		squish.pl
strip_headers.sh		strip_headers.sh
subfasta.pl		subfasta.pl
substringfasta.pl		substringfasta.pl
sumbed.pl		sumbed.pl
thumbs.sh		thumbs.sh
tm.pl		tm.pl
tm_walk.pl		tm_walk.pl
translate_ids.pl		translate_ids.pl
truncbg.pl		truncbg.pl
truncwig.pl		truncwig.pl
uc.pl		uc.pl
ucscify.sh		ucscify.sh
undofasta.pl		undofasta.pl
uniq_fa.sh		uniq_fa.sh
uniq_gtf.pl		uniq_gtf.pl
uniq_vars.sh		uniq_vars.sh
uniqbed.pl		uniqbed.pl
uniqs.sh		uniqs.sh
vstep_to_bedgraph.pl		vstep_to_bedgraph.pl

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Tue May 17 13:12:09 CDT 2011

Here's a bunch of unpolished, possibly undocumented scripts of varying ages. May the world find them useful and not terribly terrible.