Download

Download CisGenome v2.0                (Older versions: v1.2, v1.1, v1).    Installation Guide

CisGenome Windows (GUI, Browser and Core Programs All incluced)

Download CisGenome v2.0                (Older versions: v1.2, v1.1, v1)

 

CisGenome Mac OS (Core Programs Only)

Download CisGenome v2.0                (Older versions: v1.2, v1.1, v1)

CisGenome Linux (Core Programs Only)

Human: hg19, hg18, hg17

Mouse: mm9, mm8

Rat: rn4

Dog: canFam2

Cow: bosTau4

Chicken: galGal3

Zebrafish: danRer5 (NOTE: no phastCons conservation score available at this time)

             danRer4

Fly (D. melanogaster): dm3

Worm (C. elegans): ce6

Yeast (S. cerevisiae): sacCer1

Arabidopsis: TAIR9, TAIR8

             TAIR7 (NOTE: Bugs may exist in TAIR7. Using TAIR8 or TAIR9 for analysis is              recommended).

Genome Database

HUMAN

Human Genome Tiling 1.0R (14 array set): hg19, hg18

Human Genome Tiling 2.0R (7 array set): hg19, hg18

Human Promoter 1.0R: hg19, hg18

ENCODE 2.0R: hg19, hg18

 

MOUSE

Mouse Genome Tiling 2.0R (7 array set): mm9, mm8

Mouse Promoter 1.0R: mm9, mm8

 

FLY (D. melanogaster)

Drosophila Tiling 1.0R: dm3

Drosophila Tiling 2.0R: dm3

 

Worm (C. elegans)

C. elegans Tiling 1.0R: ce6

 

YEAST (S. cerevisiae)

S. cerevisiae Tiling 1.0R: sacCer1

 

ARABIDOPSIS

Arabidopsis Tiling 1.0R: TAIR9, TAIR8, TAIR7

 

 

Affymetrix Tiling Array Library Files (BPMAP files)

  

(Note: To be fully consistent with CisGenome infrastructure, using BPMAP files  downloaded from this website is recommended.)

DATA

SOFTWARE

(source code and executables)

NRSF ChIP-seq Data (from Johnson et al., Science, 316:1497-1502, 2007, Human hg17): IP, control

STAT1 ChIP-seq Data (from Robertson et al., Nature Methods, 4:651-657, 2007, Human hg18): stimulated, unstimulated

Sample Data (Please unzip the data before use)

Download CisGenome v2.0  

(Kindly contributed by Jacob Engelbrecht @ BRIC, Univ. of Copenhagen, Denmark) 

This version contains a Makefile that allows you to make cisgenome directly (instead of typing ./makefile).                  

CisGenome Unix (Make) (Core Programs Only)

To install the Mac OS / Linux version: 1. Unzip using “gzip -d *.gz”; 2. untar using “tar xvf *.tar”; 3. enter cisgenome folder; 4. compile by typing “./makefile”.

To install the Unix (Make) version: 1. Unzip using “gzip -d *.gz”; 2. untar using “tar xvf *.tar”; 3. enter cisgenome folder and src subfolder; 4. type “make”; 5. type “make bin”, everything will compile and be copied to the bin directory; 6. type “'make clean” to remove all object executable files from the src directory.