Overview

  • 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
  1. 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