PhyloAcc v1.0 – Bayesian Detection of Changes of Conservation of a Genomic Region

PhyloAcc v1.0

:: DESCRIPTION

PhyloAcc is a software to detect the shift pattern of DNA substitution rate of a genomic region and identify genomic elements accelerated in some specific species from a set of conserved elements.

::DEVELOPER

Jun Liu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOS
  • R

:: DOWNLOAD

PhyloAcc

:: MORE INFORMATION

Citation

Hu Z, Sackton TB, Edwards SV, Liu JS.
Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees.
Mol Biol Evol. 2019 May 1;36(5):1086-1100. doi: 10.1093/molbev/msz049. PMID: 30851112; PMCID: PMC6501877.

AnnotQTL 20110907 – Gather Functional and Comparative Information on a Genomic Region

AnnotQTL 20110907

:: DESCRIPTION

The AnnotQTL server is a tool designed to gather the functional annotation of genes from several institutional databases for a specific chromosomal region.

::DEVELOPER

AnnotQTL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W328-33. doi: 10.1093/nar/gkr361. Epub 2011 May 19.
AnnotQTL: a new tool to gather functional and comparative information on a genomic region.
Lecerf F1, Bretaudeau A, Sallou O, Desert C, Blum Y, Lagarrigue S, Demeure O.

GREAT 4.0.4 – Genomic Regions Enrichment of Annotations Tool

GREAT 4.0.4

:: DESCRIPTION

GREAT is a web server to analyze the functional significance of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome.

::DEVELOPER

The Bejerano Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nat Biotechnol. 2010 May;28(5):495-501. doi: 10.1038/nbt.1630. Epub 2010 May 2.
GREAT improves functional interpretation of cis-regulatory regions.
McLean CY1, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G.

CCH 20141012 – Identify Genomic Regions of Shared Ancestry

CCH 20141012

:: DESCRIPTION

CCH (Combinatorial Conflicting Homozygosity) uses dense Single Nucleotide Polymorphism (SNP) genotypes to identify regions of the genome inherited from a common ancestor among any or all subsets of a group. Analysis is rapid and can identify loci containing genes for dominant traits. CCH is robust to the presence of phenocopies and can detect undisclosed shared common ancestry.

::DEVELOPER

CCH team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Python

:: DOWNLOAD

 CCH

:: MORE INFORMATION

Citation

Combinatorial Conflicting Homozygosity (CCH) analysis enables the rapid identification of shared genomic regions in the presence of multiple phenocopies.
Levine AP, Connor TM, Oygar DD, Neild GH, Segal AW, Maxwell PH, Gale DP.
BMC Genomics. 2015 Mar 10;16:163. doi: 10.1186/s12864-015-1360-4.

regioneR 1.24.0 – Association Analysis of Genomic Regions based on Permutation Tests

regioneR 1.24.0

:: DESCRIPTION

regioneR offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features.

::DEVELOPER

Bernat Gel <bgel at imppc.org>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / WIndows
  • R
  • BioCouductor

:: DOWNLOAD

 regioneR

:: MORE INFORMATION

Citation:

regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests.
Gel B, Díez-Villanueva A, Serra E, Buschbeck M, Peinado MA, Malinverni R.
Bioinformatics. 2015 Sep 30. pii: btv562.

COUGER 1.8.2 – Identifying Co-factors Associated with Uniquely-bound Genomic Regions

COUGER 1.8.2

:: DESCRIPTION

COUGER is a framework for identifying co-factors associated with uniquely-bound genomic regions

::DEVELOPER

The Gordan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 COUGER

:: MORE INFORMATION

Citation:

COUGER-co-factors associated with uniquely-bound genomic regions.
Munteanu A, Ohler U, Gordân R.
Nucleic Acids Res. 2014 May 26. pii: gku435

Munteanu, A., & Gordan,R. (2013)
Distinguishing between genomic regions bound by paralogous transcription factors.
Research in Computational Molecular Biology 2013 (RECOMB13). 7821:145.

BiSA 0.96 – Genomic Regions Binding Sites Analysis

BiSA 0.96

:: DESCRIPTION

BiSA (Binding sites analyser) is a database driven software and stores all of its data in a relational database management system (RDBMS) such as SQL Server in Windows or PostgreSQL on Linux.

::DEVELOPER

BiSA team

:: SCREENSHOTS

bisa

:: REQUIREMENTS

  • Linux/ WIndows
  • SQL Server

:: DOWNLOAD

 BiSA

:: MORE INFORMATION

Citation

Binding sites analyser (BiSA): software for genomic binding sites archiving and overlap analysis.
Khushi M, Liddle C, Clarke CL, Graham JD.
PLoS One. 2014 Feb 12;9(2):e87301. doi: 10.1371/journal.pone.0087301.

GROK 1.1.1 – Genomic Region Operation Toolkit

GROK 1.1.1

:: DESCRIPTION

GROK is “Swiss Army knife” library for processing genomic interval data. GROK operates on genomic regions, annotated chromosomal intervals that represent sequencing short reads, gene locations, ChIP-seq peaks or other genomic features. Applications of GROK include file format conversions, set operations, overlap queries, and filtering and transformation operations. Supported file formats include BAM/SAM, BED, BedGraph, CSV, FASTQ, GFF/GTF, VCF and Wiggle.

::DEVELOPER

Systems Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • R

:: DOWNLOAD

 GROK

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2013 Jan-Feb;10(1):200-6. doi: 10.1109/TCBB.2012.170.
Genomic region operation kit for flexible processing of deep sequencing data.
Ovaska K1, Lyly L, Sahu B, J?nne OA, Hautaniemi S.

coMET – Visualisation of EWAS Results in Genomic Region

coMET

:: DESCRIPTION

The coMET package is a web-based plotting tool and R-based package to visualize EWAS (epigenome-wide association scan) results in a genomic region of interest.

::DEVELOPER

coMET team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • R

:: DOWNLOAD

 coMET

:: MORE INFORMATION

Citation:

coMET: visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns.
Martin TC, Yet I, Tsai PC, Bell JT.
BMC Bioinformatics. 2015 Apr 28;16(1):131

hot_scan – Detect Genomic Regions unusually rich in Translocation Breakpoints

hot_scan

:: DESCRIPTION

hot_scan is a free software to detect genomic regions unusually rich (hotspot) in a given pattern via scan statistics

::DEVELOPER

hot_scan team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R package
  • Perl

:: DOWNLOAD

 hot_scan

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 23. pii: btu351. [Epub ahead of print]
Identification of cromosomal translocation hotspots via scan statistics.
Silva IT1, Rosales RA2, Holanda AJ2, Nussenzweig MC3, Jankovic M3.