Sincell 1.24.0 – Analysis of Cell State Hierarchies from Single-cell RNA-seq

Sincell 1.24.0

:: DESCRIPTION

Sincell is an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq.

::DEVELOPER

Miguel Juliá <migueljuliamolina at gmail.com>, Amalio Telenti <atelenti at jcvi.org>,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Python

:: DOWNLOAD

 Sincell

:: MORE INFORMATION

Citation:

Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq.
Juliá M, Telenti A, Rausell A.
Bioinformatics. 2015 Jun 22. pii: btv368.

nextflu 1.0 – Real-time Tracking of Influenza Evolution

nextflu 1.0

:: DESCRIPTION

nextflu is designed to perform near real-time tracking of influenza virus evolution.

::DEVELOPER

bedford lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Web server

:: DOWNLOAD

 nextflu

:: MORE INFORMATION

Citation:

nextflu: real-time tracking of seasonal influenza virus evolution in humans.
Neher RA, Bedford T.
Bioinformatics. 2015 Jun 26. pii: btv381.

Logopaint 1.0 – Exploring Visualisation of Bias in Regulatory DNA or RNA Element

Logopaint 1.0

:: DESCRIPTION

Logopaint is a software of exploring the visualisation of bias in regulatory DNA or RNA element, using information context and modified logos.

::DEVELOPER

Dr Chris Brown’s Research Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • Java

:: DOWNLOAD

 Logopaint

:: MORE INFORMATION

Citation:

Bioinformatics. 2002 Apr;18(4):507-12.
Compensation for nucleotide bias in a genome by representation as a discrete channel with noise.
Schreiber M1, Brown C.

ImpG-Summary 1.0.1 – Imputation from Summary Statistics

ImpG-Summary 1.0.1

:: DESCRIPTION

ImpG-Summary  is a software package implementing methods for imputation from summary statistics and accompanying data. The software takes as input 1000 Genomes reference haplotypes and summary association statistics at a typed set of SNPs from a GWAS or meta-analysis. It outputs summary association statistics at all 1000 Genomes variants.

::DEVELOPER

Bogdan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ImpG-Summary

:: MORE INFORMATION

Citation:

Fast and accurate imputation of summary statistics enhances evidence of functional enrichment.
Pasaniuc B, Zaitlen N, Shi H, Bhatia G, Gusev A, Hirschhorn J, Strachan DP, Patterson N, Price AL.
Bioinformatics. 2014 Jul 1. pii: btu416

JASSA v4 – prediction of SUMOylation sites and SIMs

JASSA v4

:: DESCRIPTION

JASSA (Joined Advanced Sumoylation Site and Sim Analyser) is a predictor that uses a scoring system based on a Position Frequency Matrix derived from the alignment of experimental SUMOylation sites or SIMs.

::DEVELOPER

JASSA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

JASSA: a comprehensive tool for prediction of SUMOylation sites and SIMs.
Beauclair G, Bridier-Nahmias A, Zagury JF, Saïb A, Zamborlini A.
Bioinformatics. 2015 Jul 2. pii: btv403.

PubCrawler 2.40 – Update Alerting Service for PubMed and GenBank

PubCrawler 2.40

:: DESCRIPTION

PubCrawler is a free “alerting” service that scans daily updates to the NCBI Medline (PubMed) and GenBank databases.  PubCrawler helps keeping scientists informed of the current contents of Medline and GenBank, by listing new database entries that match their research interests.

::DEVELOPER

Ken Wolfe’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl

:: DOWNLOAD

 PubCrawler

:: MORE INFORMATION

AuthorReward 0.5 – Increasing Community Curation in Biological Knowledge Wikis through automated Authorship Quantification

AuthorReward 0.5

:: DESCRIPTION

AuthorReward is an extension to MediaWiki, to reward researchers’ contributions in bio-wikis by quantifying their contributions and providing explicit authorship according to their quantitative contributions.

::DEVELOPER

Zhang Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • C++ Compiler
  • PHP
  • MySQL
  • MySQL Connector/C++

:: DOWNLOAD

 AuthorReward

:: MORE INFORMATION

Citation

Dai, L., Tian, M., Wu, J.Y., Xiao, J.F., Wang, X.M., Townsend, J.P. and Zhang, Z. (2013)
AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification,
Bioinformatics, doi: 10.1093/bioinformatics/btt284.

BackCLIP 2.1 – Tool to Identify common RNA Background in PAR-CLIP Datasets

BackCLIP 2.1

:: DESCRIPTION

BackCLIP is a tool to identify the presence of common RNA background in a PAR-CLIP dataset.

::DEVELOPER

BackCLIP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 BackCLIP

:: MORE INFORMATION

Citation

BackCLIP: a tool to identify common background presence in PAR-CLIP datasets.
Reyes-Herrera PH, Speck-Hernandez CA, Sierra CA, Herrera S.
Bioinformatics. 2015 Jul 29. pii: btv442.

MetTailor 2.0 – Dynamic Block Summary and Data Normalization for Robust Analysis

MetTailor 2.0

:: DESCRIPTION

MetTailor is a software package that performs post-extraction processing steps such as cross-sample realignment and data normalization that are specifically designed to account for the experimental factors from chromatographic separation and MS analysis.

::DEVELOPER

MetTailor team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • R

:: DOWNLOAD

 MetTailor

:: MORE INFORMATION

Citation

MetTailor: Dynamic Block Summary and Intensity Normalization for Robust Analysis of Mass Spectrometry Data in Metabolomics.
Chen G, Cui L, Teo G, Ong CN, Tan CS, Choi H.
Bioinformatics. 2015 Jul 27. pii: btv434.

sydSeq 1.1.7 – Various Functions for Gene Expression Analysis

sydSeq 1.1.7

:: DESCRIPTION

sydSeq is an R package containing the functions exClust, TshrinkPlus and pMim.

::DEVELOPER

Ellis Patrick

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • R

:: DOWNLOAD

 sydSeq

:: MORE INFORMATION

Citation

Inferring data-specific micro-RNA function through the joint ranking of micro-RNA and pathways from matched micro-RNA and gene expression data.
Patrick E, Buckley M, Müller S, Lin DM, Yang JY.
Bioinformatics. 2015 Sep 1;31(17):2822-8. doi: 10.1093/bioinformatics/btv220.

Estimation of data-specific constitutive exons with RNA-Seq data.
Patrick E, Buckley M, Yang YH.
BMC Bioinformatics. 2013 Jan 29;14:31