PeakSeq 1.31 – Identify and Rank Peak Regions in ChIP-Seq Experiments

PeakSeq 1.31

:: DESCRIPTION

PeakSeq is a program for identifying and ranking peak regions in ChIP-Seq experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from a control experiment and outputs a file with peak regions ranked with increasing Q-values.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PeakSeq

:: MORE INFORMATION

Citation:

Rozowsky J, Euskirchen G, Auerbach R, Zhang Z, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein M
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
Nature Biotechnology 27, 66 – 75 (2009).

FusionHunter 1.4 – Identify Fusion Transcripts from Transcriptional Analysis of Paired-end RNA-seq

FusionHunter 1.4

:: DESCRIPTION

FusionHunter is a software which reliably identifies fusion transcripts from transcriptional analysis of paired-end RNA-seq. FusionHunter can accurately detect fusions that were previously confirmed by RT-PCR in a publicly available dataset. The purpose of FusionHunter is to identify potential fusions with high sensitivity and specificity and to guide further functional validation in the laboratory.

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 FusionHunter

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 15;27(12):1708-10. Epub 2011 May 5.
FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq.
Li Y, Chien J, Smith DI, Ma J.

NetSeed – Identify the Seed sets of Networks

NetSeed

:: DESCRIPTION

NetSeed is a software package for identifying the seed sets of networks

::DEVELOPER

the Borenstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 NetSeed

:: MORE INFORMATION

Citation

Rogan Carr and Elhanan Borenstein (2012)
NetSeed: A network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment.
Bioinformatics. doi: 10.1093/bioinformatics/btr721.

coMotif 1.0 – Identify Transcription Co-regulator Binding Sites in ChIP-seq Data

coMotif 1.0

:: DESCRIPTION

coMotif is a software of three-component mixture framework to model the joint distribution of two motifs as well as the situation where some sequences contain only one or none of the motifs.

::DEVELOPER

coMotif team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 coMotif 

:: MORE INFORMATION

Citation:

Mengyuan Xu, Clarice R. Weinberg, David M. Umbach and Leping Li
coMOTIF: a mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq Data
Bioinformatics (2011) 27 (19): 2625-2632.

CPL – An approach to identify Protein Complexes

CPL

:: DESCRIPTION

CPL is a graph clustering software, which is designed to detect protein complexes in protein-protein network (PPI). It detects the complexes by propagating labels, which is to simulate the interacting activities of proteins.

::DEVELOPER

NClab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

CPL

:: MORE INFORMATION

Citation

Journal of Computer Science and Technology November 2014, Volume 29, Issue 6, pp 1083–1093
CPL: Detecting Protein Complexes by Propagating Labels on Protein-Protein Interaction Network
Qi-Guo DaiMao-Zu GuoEmail authorXiao-Yan LiuZhi-Xia TengChun-Yu Wang

verifyBamID 1.1.3 – Identify Contamination of Sample Swap in Sequence data

verifyBamID 1.1.3

:: DESCRIPTION

verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples

::DEVELOPER

Abecasis Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 verifyBamID

:: MORE INFORMATION

Citation

G. Jun, M. Flickinger, K. N. Hetrick, Kurt, J. M. Romm, K. F. Doheny, G. Abecasis, M. Boehnke,and H. M. Kang,
Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data,
Am J Hum Genet. 2012 Nov 2;91(5):839-48. doi: 10.1016/j.ajhg.2012.09.004. (volume 91 issue 5 pp.839 – 848)

MISO 0.5.4 – RNA-Seq Experiments for Identifying Isoform Regulation

MISO 0.5.4

:: DESCRIPTION

MISO (Mixture of Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples. By modeling the generative process by which reads are produced from isoforms in RNA-Seq, the MISO model uses Bayesian inference to compute the probability that a read originated from a particular isoform.

::DEVELOPER

Christopher Burge Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  MISO

:: MORE INFORMATION

Citation

Yarden Katz, Eric T. Wang, Edoardo M. Airoldi*, Christopher B. Burge*.
Analysis and design of RNA sequencing experiments for identifying isoform regulation
Nature Methods 2010 (7, 1009-1015)

RSEG 0.4.9 – Identify Epigenomic Domains from ChIP-Seq data

RSEG 0.4.9

:: DESCRIPTION

The RSEG software package is aimed to analyze ChIP-Seq data, especially for identifying genomic regions and their boundaries marked by diffusive histone modification markers, such as H3K36me3 and H3K27me3. It can work with or without control sample. It can be used to find regions with differential histone modifications patterns, either comparsion between two cell types or between two kinds of histone modifications.

::DEVELOPER

The Smith Lab

:: SCREENSHOTS

Command

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RSEG

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Mar 15;27(6):870-1. Epub 2011 Feb 16.
Identifying dispersed epigenomic domains from ChIP-Seq data.
Song Q, Smith AD.

MONKEY 2.0 – Identify Matches to DNA Motifs in Multiple Alignments

MONKEY 2.0

:: DESCRIPTION

MONKEY is a set of programs designed to search alignments of non-coding DNA sequence for matches to matrices representing the sequence specificity of transcription factors.MONKEY employs probabilistic models of factor specificity and binding-site evolution, on which basis we compute the likelihood that putative sites are conserved and assign statistical significance to each hit.

::DEVELOPER

Alan Moses’ Computational Biology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MONKEY

:: MORE INFORMATION

Citation

Moses et. al.
MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
Genome Biol. 2004;5(12):R98

PCS 1.5 – Identify and Analyze Conserved K-mers in Pairwise Alignment

PCS 1.5

:: DESCRIPTION

PCS (Pairwise Conservation Scores) is stand-alone pakage to identify and analyze conserved k-mers in pairwise alignment. This program shows high performance for identifying miRNA seed binding sites in 3′-UTRs.

::DEVELOPER

Bioinformatics & Intelligent Information Processing Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Perl 

:: DOWNLOAD

 PCS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Nov 8;8:432.
Identifications of conserved 7-mers in 3′-UTRs and microRNAs in Drosophila.
Gu J, Fu H, Zhang X, Li Y.