GitHub - Jia21/jmtools: This is a sandbox of scripts that I have created (~98%) or gathered from others since 2007. It is only stored here for utility and posterity. They are all constantly being updated, thus they should be treated as work-in-progress - raw and unpolished. Please ask for permission before publishing.

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This is a sandbox of scripts that I have created (~98%) or gathered from others since 2007. It is only stored here for utility and posterity. They are all constantly being updated, thus they should be treated as work-in-progress - raw and unpolished. Please ask for permission before publishing.

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Name		Name	Last commit message	Last commit date
Latest commit History 239 Commits
alex_cnvScripts		alex_cnvScripts
alex_pgenome_checks		alex_pgenome_checks
alleleSeq_cnvScript		alleleSeq_cnvScript
alleleSeq_wrap		alleleSeq_wrap
3.FIG.motif.gain.loss.fromYao.pl		3.FIG.motif.gain.loss.fromYao.pl
BOWTIE.sh		BOWTIE.sh
R4fisherstest		R4fisherstest
R4fisherstest.axSamples		R4fisherstest.axSamples
R4fisherstest.axSamples.aFile		R4fisherstest.axSamples.aFile
TFMpvalue-pv2sc		TFMpvalue-pv2sc
TFMpvalue-sc2pv		TFMpvalue-sc2pv
TGnearMonoSearch4vik		TGnearMonoSearch4vik
aallele_incomp		aallele_incomp
affygtc2tg		affygtc2tg
alignedreads2fpkm4cbb752		alignedreads2fpkm4cbb752
alleleAddPop		alleleAddPop
alleleBed2ratio_asb		alleleBed2ratio_asb
alleleBed2ratio_ase		alleleBed2ratio_ase
alleleBinGene		alleleBinGene
alleleBinomial		alleleBinomial
alleleCombineCounts_asb.sh		alleleCombineCounts_asb.sh
alleleCombineCounts_ase.sh		alleleCombineCounts_ase.sh
alleleCountIndConfident		alleleCountIndConfident
alleleCountsPeakIntersect-chr.sh		alleleCountsPeakIntersect-chr.sh
alleleCountsPeakIntersect.sh		alleleCountsPeakIntersect.sh
alleleCountsPeakIntersect_loop-chr.sh		alleleCountsPeakIntersect_loop-chr.sh
alleleCountsPeakIntersect_loop.sh		alleleCountsPeakIntersect_loop.sh
alleleDB.update.sh		alleleDB.update.sh
allelePval2minN		allelePval2minN
alleleRnaCounts2bed.sh		alleleRnaCounts2bed.sh
alleleRnaCounts2bed_loop.sh		alleleRnaCounts2bed_loop.sh
alleleSeqPeak		alleleSeqPeak
allele_readdepth_table_beta_n_binomial_distribution_gradient_custom_io_timur.R		allele_readdepth_table_beta_n_binomial_distribution_gradient_custom_io_timur.R
alleledb-1-infrastructure.sh		alleledb-1-infrastructure.sh
alleledb-2a-mat.sh		alleledb-2a-mat.sh
alleledb-2b-pat.sh		alleledb-2b-pat.sh
alleledb-3-run-alleleseq.sh		alleledb-3-run-alleleseq.sh
alleledb-newpipeline		alleledb-newpipeline
alleledb.sh		alleledb.sh
alleledb_ThunderByRob.jar		alleledb_ThunderByRob.jar
alleledb_alleleseqBetabinomial.R		alleledb_alleleseqBetabinomial.R
alleledb_alleleseqOutput2betabinomFormat.sh		alleledb_alleleseqOutput2betabinomFormat.sh
alleledb_bedbowtie2fastq		alleledb_bedbowtie2fastq
alleledb_bowtie2bed		alleledb_bowtie2bed
alleledb_bowtie2fastq		alleledb_bowtie2fastq
alleledb_calcAllelicBias		alleledb_calcAllelicBias
alleledb_calcOverdispersion.R		alleledb_calcOverdispersion.R
alleledb_enrichment_cleanup.sh		alleledb_enrichment_cleanup.sh
alleledb_filter_input.sh		alleledb_filter_input.sh
alleledb_flipread2fastq		alleledb_flipread2fastq
alleledb_map.back.ref.wrapper.sh		alleledb_map.back.ref.wrapper.sh
alleledb_multis-and-unaligneds-wrapper.sh		alleledb_multis-and-unaligneds-wrapper.sh
alleleseq_in_betabinomial_custom_io_2bugfixed_timur.R		alleleseq_in_betabinomial_custom_io_2bugfixed_timur.R
allelicbias-check		allelicbias-check
allelicbias-check-by-sites		allelicbias-check-by-sites
allelicbias-check-cmp-by-reads		allelicbias-check-cmp-by-reads
allelicbias-check-smallfastq		allelicbias-check-smallfastq
apt-tsv-join		apt-tsv-join
ariffile2tsv_incompl		ariffile2tsv_incompl
beagle2tg		beagle2tg
bins2perlcase_nicks		bins2perlcase_nicks
birdsuite-sort.sh		birdsuite-sort.sh
blast2tsv		blast2tsv
blatsplitmerge2fasta		blatsplitmerge2fasta
blosum		blosum
bsub-make-bash.sh		bsub-make-bash.sh
bsub-make-betabinomial-gradient.sh		bsub-make-betabinomial-gradient.sh
bsub-make-betabinomial.sh		bsub-make-betabinomial.sh
bsub-make-plus-bash.sh		bsub-make-plus-bash.sh
bsub-make-plus.sh		bsub-make-plus.sh
bsub-make-singleline.sh		bsub-make-singleline.sh
bsub-make.sh		bsub-make.sh
bsub-script-rdy-jmtest.sh		bsub-script-rdy-jmtest.sh
calcAverage		calcAverage
calcDihedral.c		calcDihedral.c
calc_overdispersion_nongradient.R		calc_overdispersion_nongradient.R
chainSwap		chainSwap
chisq2pval		chisq2pval
chisq2pval-new-incomp		chisq2pval-new-incomp
chisq2pval-new-new-incompl		chisq2pval-new-new-incompl
classifyPromoter		classifyPromoter
correlation4vik		correlation4vik
create-script-and-qsub.sh		create-script-and-qsub.sh
create-script-and-qsub2.sh		create-script-and-qsub2.sh
create-script-erwin.sh		create-script-erwin.sh
create-split-chr-qsub-main.sh		create-split-chr-qsub-main.sh
create-split-chr-qsub.sh		create-split-chr-qsub.sh
dbsnp_sub-snpinduse+snppopuse		dbsnp_sub-snpinduse+snppopuse
dbsnp_sub-snpinduse-incompl		dbsnp_sub-snpinduse-incompl
dbsnp_sub-snppopuse-incompl		dbsnp_sub-snppopuse-incompl
deal4ekta		deal4ekta
devindri		devindri
doit.sh		doit.sh
dstool		dstool
dstool_dbsnp		dstool_dbsnp
eclipGen_incompl		eclipGen_incompl
eigenpca2fpca		eigenpca2fpca
ensemblFetchProteinFasta.ip		ensemblFetchProteinFasta.ip
ensembl_ancestral_allele_motifvar		ensembl_ancestral_allele_motifvar
ensembl_fetch_protein_fasta_sequences.pl		ensembl_fetch_protein_fasta_sequences.pl