clusterProfiler 3.14.0 – Statistical Analysis and Visulization of Functional Profiles for Genes and Gene Clusters

clusterProfiler 3.14.0

:: DESCRIPTION

clusterProfiler implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.

::DEVELOPER

Guangchuang YU,, Li-Gen Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

  clusterProfiler

:: MORE INFORMATION

Citation

OMICS. 2012 May;16(5):284-7. doi: 10.1089/omi.2011.0118. Epub 2012 Mar 28.
clusterProfiler: an R package for comparing biological themes among gene clusters.
Yu G1, Wang LG, Han Y, He QY.

SelEstim 1.1.7 – Detecting and Measuring Selection from Gene Frequency data

SelEstim 1.1.7

:: DESCRIPTION

SelEstim is a software to detect signatures of selection from gene frequency data and measure the selection intensity

::DEVELOPER

Centre de Biologie et Gestion des Populations (CBGP)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  MacOsX / Linux
  • R

:: DOWNLOAD

 SelEstim

:: MORE INFORMATION

Citation

Genetics. 2014 Mar;196(3):799-817. doi: 10.1534/genetics.113.152991. Epub 2013 Dec 20.
Detecting and measuring selection from gene frequency data.
Vitalis R1, Gautier M, Dawson KJ, Beaumont MA.

desiRm – Designing siRNA for Silencing a Gene

desiRm

:: DESCRIPTION

desiRm is a webserver for designing highly effective siRNA for silencing a gene. This tool will be helpful to design siRNA to degrade disease isoform of heterozygous single nucleotide polymorphism gene without depleting the wild type protein.

::DEVELOPER

desiRm team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2011;6(8):e23443. doi: 10.1371/journal.pone.0023443. Epub 2011 Aug 10.
Designing of highly effective complementary and mismatch siRNAs for silencing a gene.
Ahmed F1, Raghava GP.

Pan-Tetris 0.9 – Interactive Pan-genome Visualization

Pan-Tetris 0.9

:: DESCRIPTION

Pan-Tetris is our interactive software tool that enables the visual inspection of gene occurrences in a pan-genome table. It allows the user to modify the composition of such pan gene groups with an aggregation technique that is inspired by the famous Tetris game.

::DEVELOPER

Research Group “Integrative Transcriptomics” , Center for Bioinformatics Tübingen, University of Tübingen

:: SCREENSHOTS

Pan-Tetris

:: REQUIREMENTS

  • Linux/MacOS / WIndows
  • Java

:: DOWNLOAD

 Pan-Tetris

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2015;16 Suppl 11:S3. doi: 10.1186/1471-2105-16-S11-S3. Epub 2015 Aug 13.
Pan-Tetris: an interactive visualisation for Pan-genomes.
Hennig A, Bernhardt J, Nieselt K.

FragGeneScan 1.31 – Predicting Genes in Short and Error-prone Reads

FragGeneScan 1.31

:: DESCRIPTION

FragGeneScan is an application for finding (fragmented) genes in short reads.The software combines sequencing error models and codon usages in a hidden Markov model to improve the prediction of protein-coding region in short reads.

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  FragGeneScan

:: MORE INFORMATION

Citation:

Mina Rho, Haixu Tang, and Yuzhen Ye.
FragGeneScan: Predicting Genes in Short and Error-prone Reads.
Nucl. Acids Res., 2010 doi: 10.1093/nar/gkq747

ExonHunter 1.07 – Comparative Gene Finder

ExonHunter 1.07

:: DESCRIPTION

ExonHunter is a comprehensive gene finder based on hidden Markov models allowing use of variety of additional sources of information (ESTs, proteins, genome-genome comparison, repeats, and more).

:: DEVELOPER

Computational Biology @ Comenius University in Bratislava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 ExonHunter

:: MORE INFORMATION

Citation

ExonHunter: a comprehensive approach to gene finding.
Brejová B, Brown DG, Li M, Vinar T.
Bioinformatics. 2005 Jun;21 Suppl 1:i57-65.

NLDMseq – Expression Calculation at both Gene and Isoform levels from RNA-seq data given a Reference Transcriptom

NLDMseq

:: DESCRIPTION

NLDMseq is a bioinformatics tool for expression calculation at both gene and isoform levels from RNA-seq data by considering isoform- and exon-specific read sequencing rate.

::DEVELOPER

Xuejun Liu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python

:: DOWNLOAD

 NLDMseq

:: MORE INFORMATION

Citation

Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate.
Liu X, Shi X, Chen C, Zhang L.
BMC Bioinformatics. 2015 Oct 16;16(1):332. doi: 10.1186/s12859-015-0750-6.

OEFinder 0.0.2 – Identify Ordering Effect Genes in Single Cell RNA-seq data

OEFinder 0.0.2

:: DESCRIPTION

OEFinder is a user interface to identify and visualize ordering effects in single-cell RNA-seq data.

::DEVELOPER

Ning Leng

:: SCREENSHOTS

OEFinder

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 OEFinder

:: MORE INFORMATION

Citation

OEFinder: A user interface to identify and visualize ordering effects in single-cell RNA-seq data.
Leng N, Choi J, Chu LF, Thomson JA, Kendziorski C, Stewart R.
Bioinformatics. 2016 Jan 6. pii: btw004.

JODA 1.33.0 – Quantifying Gene Deregulation using Knowledge

JODA 1.33.0

:: DESCRIPTION

JODA (Joint deregulation analysis) proves advantageous over separate analysis of the cell populations and analysis without incorporation of knowledge.

:: DEVELOPER

JODA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 JODA

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Jun 21;12:249. doi: 10.1186/1471-2105-12-249.
Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data.
Szczurek E1, Markowetz F, Gat-Viks I, Biecek P, Tiuryn J, Vingron M.

sampletrees 20151127 / Rsampletrees 1.0.2 – Sampling Gene Genealogies Conditional on SNP Genotype data

sampletrees 20151127 / Rsampletrees 1.0.2

:: DESCRIPTION

The program sampletrees is a Markov chain Monte Carlo sampler of gene genealogies conditional on either phased or unphased SNP genotype data. The companion program Rsampletrees is for pre- and post-processing of sampletrees files, including setting up the files for sampletrees and storing and plotting the output of a sampletrees run.

::DEVELOPER

SFU Statistical Genetics working group

:: REQUIREMENTS

:: DOWNLOAD

 sampletrees / Rsampletrees 

:: MORE INFORMATION

Citation

sampletrees and Rsampletrees: Sampling gene genealogies conditional on SNP genotype data.
Burkett KM, McNeney B, Graham J.
Bioinformatics. 2016 Jan 18. pii: btv763.