| Software and Algorithms |
|
|
| PHAST and RPHAST |
Hubisz et al., 2011 |
http://compgen.cshl.edu/phast/; http://compgen.cshl.edu/rphast/
|
| BioMart |
Bioconductor |
http://bioconductor.org/packages/release/bioc/html/biomaRt.html |
| VCD |
Meyer et al., 2006 |
https://cran.r-project.org/web/packages/vcd/index.html |
| Biostrings |
Bioconductor |
http://bioconductor.org/packages/release/bioc/html/Biostrings.html |
| LOLA |
Bioconductor |
https://bioconductor.org/packages/release/bioc/html/LOLA.html |
| GenomicRanges |
Bioconductor |
https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html |
| MotifDB |
Bioconductor |
http://bioconductor.org/packages/release/bioc/html/MotifDb.html |
| PWMEnrich |
Bioconductor |
http://bioconductor.org/packages/release/bioc/html/PWMEnrich.html |
| Seaview |
Seaview |
http://doua.prabi.fr/software/seaview |
| GREAT |
McLean et al., 2010 |
http://bejerano.stanford.edu/great/public/html/ |
| Galaxy |
Galaxy |
https://usegalaxy.org |
| Circlize |
CRAN |
https://cran.r-project.org/web/packages/circlize/index.html |
| ChIP-Atlas |
Okietal., 2018 |
http://chip-atlas.org |
| SuperExactTest |
CRAN |
https://cran.r-project.org/web/packages/SuperExactTest/index.html |
| Custom python and R scripts |
Gregg Lab, University of Utah |
Available upon request |
| Other |
|
|
| Multiple alignments of 59 vertebrate genomes with Mouse |
UCSC |
http://hgdownload.cse.ucsc.edu/goldenpath/mm10/multiz60way/maf/ |
| Multiple alignments of 59 vertebrate genomes with Mouse Neutral Model |
UCSC |
http://hgdownload.cse.ucsc.edu/goldenpath/mm10/phastCons60way/mm10.60way.phastCons.mod |
| BMI risk loci identified by GWAS |
Ghosh and Bouchard, 2017; Turcot et al., 2018
|
N/A |
| PWS DE genes in the hypothalamus |
Bochukova et al., 2018 |
N/A |
| ENCODE hg19 bedfiles for DNase HS (ENCFF751YPI), distal H3K27ac (ENCFF786PWS), H3K9ac (ENCFF690JTO), proximal H3K4me3 (ENCFF140OFS), distal and proximal TF binding sites (ENCFF787QYS), proximal H3K4me1 (ENCFF076KTT), USCS hg19 2K promoter table, intron table and coding exon table |
UCSC Table Browser |
https://genome.ucsc.edu/cgi-bin/hgTables |
