taolib

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• Attention

This my personal code repository. I haven't tested them fully. So I can't guarantee they works...

• Ancient README

• WebApp list:

1. CistromeDB

The CistromeDB website based on Django framework. Check CistromeDB/INSTALL.txt for detail.

• Exectuables list:

1. motif_enrich.py Usage: motif_enrich.py [options]

Calculate the motif enrichment measured in foldchange and p-value for one BED file and one reference BED file

Options: --version show program's version number and exit -h, --help Show this help message and exit. -s SPECIES, --species=SPECIES species, must be "mm8" or "hg18" -i IFILE, --ifile=IFILE input BED file, e.g. the ChIP regions -r RFILE, --rfile=RFILE input reference BED file, e.g. the tiled regions. [optional] if not set, use the whole genome as reference -c CUTOFF, --cutoff=CUTOFF cutoff for the motif scan score -d IDIR, --idir=IDIR input directory for binary Motif Scan Results files -a, --all If set, also show the depleted motifs. Default, not show --minfc=MINFC minimum foldchange for motif enrichment, default:0 --maxp=MAXP maximum p-value for motif enrichment, default:1 --minpercent=MINPERCENT minimum percentage of input BED regions containing motif, default:5 --maxpercent=MAXPERCENT maximum percentage of input BED regions containing motif, default:300 --verbose=VERBOSE Name of a directory. if set, save verbose information in the direcotry. -o OFILE, --ofile=OFILE output file 2. ceas.py Usage: ceas.py [options]

CEAS -- Cis-regulatory Element Annotation System

Options: --version show program's version number and exit -h, --help Show this help message and exit. --chip-res=CHIP_RES ChIP resolution, default: 600 bp --bg-res=BG_RES Genome BG resolution, default: 100 bp --promoter=PROMOTER Promoter range size, default: 3000 bp --bipromoter=BIPROMOTER Bidirectional-promoter range size, default: 5000 bp --downstream=DOWNSTREAM Downstream range size, default: 3000 bp --nopf No profiling is run and the options regarding profiiling will not be effective if this switch is set --rel-dist=REL_DIST Relative distance to TSS/TTS for gene profiling, default: 3000 bp --metagene-size=METAGENE_SIZE Metagene size, default: 3000 bp --pf-res=PF_RES Profiling resolution, default: 50 bp --gn-groups=GN_GROUPS Gene-group file names (eg, top10.txt,bottom10.txt), default: all genes --gn-group-names=GN_NAMES Gene-group names for profiling (eg, top 10%,bottom 10%), default: None -a, --alt-gn-name 'name2' in refGene table is used if set. This flag is meaningful only if --gn-groups is set. -i IFILE, --ifile=IFILE input BED file, e.g. the ChIP regions -w WFILE, --wfile=WFILE input wiggle file. -n NCBED, --ncbed=NCBED noncoding region BED file, default: None -g GDB, --gene-db=GDB Gene annotation database file from Cistrome website --gt=GT optional genome table. default: None -o OFILE, --ofile=OFILE output R script. default: stdout --verbose=VERBOSE Name of a directory. if set, save verbose information in the direcotry.

3. qc_chIP.py Usage: qc_chIP.py [options]

QC for two replicates of ChIP-chip experiment. Do both peak level and probe level calculations.

Options: --version show program's version number and exit -h, --help Show this help message and exit. -p PEAK1, --peak1=PEAK1 peak file in xls format for #1 replicate -q PEAK2, --peak2=PEAK2 peak file in xls format for #2 replicate -x WIG1, --wig1=WIG1 wiggle file for #1 replicate -y WIG2, --wig2=WIG2 wiggle file for #2 replicate -r RFILE, --rfile=RFILE R output file -f FORMAT, --format=FORMAT ma2c, mat or macs, default: ma2c -s STEP, --step=STEP number of steps to calculate cor based on some score ranges, default: 5

4. qc_chIP2.py Usage: qc_chIP2.py [options]

QC for two replicates of ChIP-chip experiment. Only for naive overall probe level calculation.

Options: --version show program's version number and exit -h, --help Show this help message and exit. -x WIG1, --wig1=WIG1 wiggle file for #1 replicate -y WIG2, --wig2=WIG2 wiggle file for #2 replicate -r RFILE, --rfile=RFILE R output file. If not set, do not save R file. -s STEP, --step=STEP probe step, default: 100 -f FORMAT, --format=FORMAT ma2c, mat or macs, default: ma2c

5. count_probes_in_peaks.py Usage: count_probes_in_peaks.py [options]

Summarize ChIP-chip experiment. Calculate how many probes are included in peak regions.

Options: --version show program's version number and exit -h, --help Show this help message and exit. -p PEAK1, --peak1=PEAK1 peak file in xls format for #1 replicate -x WIG1, --wig1=WIG1 wiggle file for #1 replicate -o OFILE, --ofile=OFILE output file -f FORMAT, --format=FORMAT ma2c, mat or macs, default: ma2c

6. count_probes_in_ranges.py Usage: count_probes_in_ranges.py [options]

Summarize ChIP-chip experiment. Calculate how many probes fall into certain score ranges '(-inf,-1],(-1,0],(0,+1],(+1,+inf)'.

Options: --version show program's version number and exit -h, --help Show this help message and exit. -x WIG1, --wig1=WIG1 wiggle file for #1 replicate -o OFILE, --ofile=OFILE output file

7. xyz2image.py

Restore the microarray image.

need 1 parameter: xyz2image.py <X-Y-Value-file>

X-Y-Value-file is a tab-delimited file with 1st column as X-corrdinates, 2nd column as Y, and 3rd column as log-ratio value