DeMixT 1.6.0 – Deconvolution on Transcriptome data from a mixture of two or three components

DeMixT 1.6.0

:: DESCRIPTION

DeMixT is a deconvolution framework for mixed transcriptomes from heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms.

::DEVELOPER

Statistical Bioinformatics Lab, The University of Texas M. D. Anderson Cancer Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX
  • R package
  • BioCOnductor

:: DOWNLOAD

 DeMixT

:: MORE INFORMATION

Citation

Wang Z, Cao S, Morris JS, Ahn J, Liu R, Tyekucheva S, Gao F, Li B, Lu W, Tang X, Wistuba II, Bowden M, Mucci L, Loda M, Parmigiani G, Holmes CC, Wang W.
Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration.
iScience. 2018 Nov 30;9:451-460. doi: 10.1016/j.isci.2018.10.028. Epub 2018 Nov 2. PMID: 30469014; PMCID: PMC6249353.

Bioinformatics. 2013 Aug 1;29(15):1865-71. doi: 10.1093/bioinformatics/btt301.
DeMix: deconvolution for mixed cancer transcriptomes using raw measured data.
Ahn J, Yuan Y, Parmigiani G, Suraokar MB, Diao L, Wistuba II, Wang W.

ScreenBEAM 1.0 – Functional Genomics Screens via Bayesian Hierarchical Modeling

ScreenBEAM 1.0

:: DESCRIPTION

ScreenBEAM is an R package to do gene-level meta-anlaysis of high-throughput functional genomics RNAi or CRISPR screening data. Both microarray and NGS data are supported

::DEVELOPER

Jiyang Yu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 ScreenBEAM

:: MORE INFORMATION

Citation

ScreenBEAM: a Novel Meta-Analysis Algorithm for Functional Genomics Screens via Bayesian Hierarchical Modeling.
Yu J, Silva J, Califano A.
Bioinformatics. 2015 Sep 28. pii: btv556.

Cytoscape.js 3.18.2 – Graph Theory Library for Visualisation and Analysis

Cytoscape.js 3.18.2

:: DESCRIPTION

Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser.

::DEVELOPER

the Donnelly Centre at the University of Toronto.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Weindows/Linux/MacOsX
  • JavaScript

:: DOWNLOAD

 Cytoscape.js

:: MORE INFORMATION

Citation

Cytoscape.js: a graph theory library for visualisation and analysis.
Franz M, Lopes CT, Huck G, Dong Y, Sumer O, Bader GD.
Bioinformatics. 2015 Sep 28. pii: btv557.

pGenN – Gene Normalization Tool for Plant Genes and Proteins in Scientific Literature

pGenN

:: DESCRIPTION

pGenN is a system specifically designed for plant gene normalization. This pGenN website enables user search gene normalization information by keywords, a list of PMIDs, or UniProt ACs in the database. The results (Gene names and corresponding UniProt ACs) are displayed in sortable tables with text evidence and downloadable for further research.

::DEVELOPER

BioNLP and Text Mining Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

pGenN, a Gene Normalization Tool for Plant Genes and Proteins in Scientific Literature.
Ding R, Arighi CN, Lee JY, Wu CH, Vijay-Shanker K.
PLoS One. 2015 Aug 10;10(8):e0135305. doi: 10.1371/journal.pone.0135305.

miRTex – Text Mining System for miRNA-Gene Relation Extraction

miRTex

:: DESCRIPTION

miRTex is a text-mining system that extracts miRNA-gene regulation relations and miRNA-target relations from literature.

::DEVELOPER

Center for Bioinformatics and Computational Biology, University of Delaware

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

miRTex: A Text Mining System for miRNA-Gene Relation Extraction.
Li G, Ross KE, Arighi CN, Peng Y, Wu CH, Vijay-Shanker K.
PLoS Comput Biol. 2015 Sep 25;11(9):e1004391. doi: 10.1371/journal.pcbi.1004391.

FunRich 3.1.4 – Functional Enrichment analysis tool

FunRich 3.1.4

:: DESCRIPTION

FunRich is a stand-alone software tool used mainly for functional enrichment and interaction network analysis of genes and proteins.

::DEVELOPER

FunRich team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 FunRich

:: MORE INFORMATION

Citation

FunRich: An open access standalone functional enrichment and interaction network analysis tool.
Pathan M, Keerthikumar S, Ang CS, Gangoda L, Quek CY, Williamson NA, Mouradov D, Sieber OM, Simpson RJ, Salim A, Bacic A, Hill AF, Stroud DA, Ryan MT, Agbinya JI, Mariadason JM, Burgess AW, Mathivanan S.
Proteomics. 2015 Aug;15(15):2597-601. doi: 10.1002/pmic.201400515

diCal 1.3 / diCal-IBD 1.0 – Predicts Identical by Descent Tracts using Sequence data

diCal 1.3 / diCal-IBD 1.0

:: DESCRIPTION

diCal is a scalable demographic inference method based on the sequentially Markov conditional sampling distribution framework.

diCal-IBD can be used for predicting identical by descent (IBD) tracts in sequence data. It provides means for calculating the accuracy of the prediction, if the true tracts are available, plotting of the predicted tracts, their TMRCA (time to the most recent common ancestor) and corresponding posterior probabilities, and identification of putative recent positive selection through investigation of average IBD sharing

::DEVELOPER

The Biophysics Graduate Group, Yun S. Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

  diCal-IBD , diCal

:: MORE INFORMATION

Citation

Genetics. 2013 Jul;194(3):647-62. doi: 10.1534/genetics.112.149096. Epub 2013 Apr 22.
Estimating variable effective population sizes from multiple genomes: a sequentially markov conditional sampling distribution approach.
Sheehan S1, Harris K, Song YS.

diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals.
Tataru P, Nirody JA, Song YS.
Bioinformatics. 2014 Aug 21. pii: btu563

FoCuS-point 1.16.197 – Python TCSPC FCS data Visualiser

FoCuS-point 1.16.197

:: DESCRIPTION

FoCuS-point utilises advanced time-correlated single-photon counting (TCSPC) correlation algorithms along with time-gated filtering and innovative data visualisation.

::DEVELOPER

Dominic Waithe

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 FoCuS-point

:: MORE INFORMATION

Citation

FoCuS-point: Software for STED Fluorescence Correlation and Time-Gated Single Photon Counting.
Waithe D, Clausen MP, Sezgin E, Eggeling C.
Bioinformatics. 2015 Nov 20. pii: btv687.

Insyght – Conserved Synteny Homolog Browser

Insyght

:: DESCRIPTION

Insyght is a browser that helps navigate among abundant homologies, syntenies and genes annotations.

::DEVELOPER

Insyght team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Synchronized navigation and comparative analyses across Ensembl complete bacterial genomes with INSYGHT.
Lacroix T, Thérond S, Rugeri M, Nicolas P, Gendrault A, Loux V, Gibrat JF.
Bioinformatics. 2015 Nov 24. pii: btv689.

sdef 1.7 – Synthesizing List of Differentially Expressed Features

sdef 1.7

:: DESCRIPTION

sdef performs two tests to evaluate if the experiments are associated and returns a list of interesting features common to all the experiments.

::DEVELOPER

Alberto Cassese <alberto.cassese at maastrichtuniversity.nl>, Marta Blangiardo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/  MacOSX / Windows
  • R

:: DOWNLOAD

 sdef

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 May 20;11:270. doi: 10.1186/1471-2105-11-270.
sdef: an R package to synthesize lists of significant features in related experiments.
Blangiardo M1, Cassese A, Richardson S.