EMPeror 1.0.0-beta.20 – Analysis of High Throughput Microbial Ecology datasets

EMPeror 1.0.0-beta.20

:: DESCRIPTION

Emperor is an interactive next generation tool for the analysis, visualization and understanding of high throughput microbial ecology datasets.

::DEVELOPER

Knight Lab

:: SCREENSHOTS

 EMPeror

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python
  • Numpy
  • qcli

:: DOWNLOAD

 EMPeror

 :: MORE INFORMATION

Citation

EMPeror: a tool for visualizing high-throughput microbial community data.
Vázquez-Baeza Y, Pirrung M, Gonzalez A, Knight R.
Gigascience. 2013 Nov 26;2(1):16. doi: 10.1186/2047-217X-2-16.

SbacHTS v5 – Spatial background correction for High-Throughput RNAi Screening

SbacHTS v5

:: DESCRIPTION

SbacHTS is a software for visualization, estimation and correction of spatial background noises of RNAi screening experiment results.

::DEVELOPER

The Quantitative Biomedical Research Center 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 SbacHTS

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Sep 1;29(17):2218-20. doi: 10.1093/bioinformatics/btt358. Epub 2013 Jun 28.
SbacHTS: spatial background noise correction for high-throughput RNAi screening.
Zhong R1, Kim MS, White MA, Xie Y, Xiao G.

Piranha 1.2.1 – Peak-caller for CLIP- and RIP-Seq high-throughput Protein-RNA interaction data

Piranha 1.2.1

:: DESCRIPTION

Piranha is a peak-caller for CLIP- and RIP-Seq high-throughput protein-RNA interaction data. It accepts input in BED or BAM format and identifies regions of significant enrichment for reads. Piranha can also optionally incorporate additional external covariates into the peak-calling process, and identify sites of differential binding occupancy between cell types, conditions or development stages.

::DEVELOPER

The Smith Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

 Piranha

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Dec 1;28(23):3013-20. doi: 10.1093/bioinformatics/bts569. Epub 2012 Sep 28.
Site identification in high-throughput RNA-protein interaction data.
Uren PJ, Bahrami-Samani E, Burns SC, Qiao M, Karginov FV, Hodges E, Hannon GJ, Sanford JR, Penalva LO, Smith AD.

FALCON@home – High-throughput Protein Structure Prediction server

FALCON@home

:: DESCRIPTION

The design of FALCON@home is based on the observation that a structural template, especially for remote homologous proteins, consists of conserved regions interweaved with highly-variable regions.

::DEVELOPER

Bioinformatics Lab, Institute of Computing Technology Chinese Academy of Sciences

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition.
Wang C, Zhang H, Zheng WM, Xu D, Zhu J, Wang B, Ning K, Sun S, Li SC, Bu D.
Bioinformatics. 2015 Oct 10. pii: btv581.

ShortRead 1.42.0 – Classes and Methods for High-throughput Short-read Sequencing data

ShortRead 1.42.0

:: DESCRIPTION

ShortRead is a package for input, quality assessment, manipulation and output of high-throughput sequencing data.

:: DEVELOPER

ShortRead team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX/Windows
  • R package
  • BioConductor

:: DOWNLOAD

 ShortRead

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Oct 1;25(19):2607-8. doi: 10.1093/bioinformatics/btp450.
ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data.
Morgan M, Anders S, Lawrence M, Aboyoun P, Pagès H, Gentleman R.

Heat*seq – High-throughput Sequencing Experiment Comparison with Public data

Heat*seq

:: DESCRIPTION

Heat*seq is a web-tool that allows genome scale comparison of high throughput experiments (ChIP-seq, RNA-seq and CAGE) provided by a user, to the data in the public domain.

::DEVELOPER

Heat*seq team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Heat*seq

:: MORE INFORMATION

Citation:

Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data.
Devailly G, Mantsoki A, Joshi A.
Bioinformatics. 2016 Jul 4. pii: btw407.

htSeqTools 1.31.0 – Quality Control, Visualization and Processing for High-Throughput Sequencing data

htSeqTools 1.31.0

:: DESCRIPTION

htSeqTools is a Bioconductor package with quality assessment, processing and visualization tools for high-throughput sequencing data, with emphasis in ChIP-seq and RNA-seq studies.

::DEVELOPER

Evarist Planet, Camille Stephan-Otto, Oscar Reina <oscar.reina at irbbarcelona.org>, Oscar Flores, David Rossell

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • R
  • Bioconductor

:: DOWNLOAD

 htSeqTools

:: MORE INFORMATION

Citation

htSeqTools: high-throughput sequencing quality control, processing and visualization in R.
Planet E, Attolini CS, Reina O, Flores O, Rossell D.
Bioinformatics. 2012 Feb 15;28(4):589-90. doi: 10.1093/bioinformatics/btr700.

EpiRegNet – Epigenetic Regulatory Network from High Throughput Gene Expression

EpiRegNet

:: DESCRIPTION

EpiRegNet aims to build a transcriptional regulatory network composing of histone modification and transcription factor binding in promoters and interactions between factors in these two fields.

::DEVELOPER

JJWang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Epigenetics. 2011 Dec;6(12):1505-12. doi: 10.4161/epi.6.12.18176.
EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans.
Wang LY1, Wang P, Li MJ, Qin J, Wang X, Zhang MQ, Wang J.

PLNseq 1.0 – Poisson Lognormal Distribution for High-throughput matched RNA-sequencing Read Count data

PLNseq 1.0

:: DESCRIPTION

The PLNseq package conducts differential expression (DE) analysis using high throughput  RNA-seq read count data generated from correlated samples.

::DEVELOPER

Hong Zhang @Fudan University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

PLNseq

:: MORE INFORMATION

Citation

Stat Med. 2015 Apr 30;34(9):1577-89. doi: 10.1002/sim.6449. Epub 2015 Jan 30.
PLNseq: a multivariate Poisson lognormal distribution for high-throughput matched RNA-sequencing read count data.
Zhang H1, Xu J, Jiang N, Hu X, Luo Z.

Vidjil 2015.10.2 – High-throughput V(D)J Repertoire Analysis

Vidjil 2015.10.2

:: DESCRIPTION

Vidjil processes high-throughput sequencing data to extract V(D)J junctions and gather them into clones. This analysis is based on a seed heuristics and is fast and scalable, as, in the first phase, no alignment is performed with database germline sequences.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux
  • C++ Compiler

:: DOWNLOAD

  Vidjil

:: MORE INFORMATION

Citation

Mathieu Giraud, Mikaël Salson, Marc Duez, Céline Villenet, Sabine Quief, Aurélie Caillault, Nathalie Grardel, Christophe Roumier, Claude Preudhomme, Martin Figeac,
Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing,
BMC Genomics, 15:409, doi:10.1186/1471-2164-15-409