compcodeR 1.26.1 – Benchmarking Differential Expression Methods for RNA-seq data

compcodeR 1.26.1

:: DESCRIPTION

compcodeR is an R package for comparing the results of multiple differential expression analysis methods applied to a common RNAseq data set. It also contains functionalities for simulating realistic count matrices and interfaces to several of the most widely used differential expression analysis methods for RNAseq data.

::DEVELOPER

Charlotte Soneson <Charlotte.Soneson at isb-sib.ch>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 compcodeR

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 9. [Epub ahead of print]
compcodeR – an R package for benchmarking differential expression methods for RNA-seq data.
Soneson C.

Mockrobiota – Public Resource for Microbiome Bioinformatics Benchmarking

Mockrobiota

:: DESCRIPTION

Mockrobiota is a public resource for microbiome bioinformatics benchmarking using artificially constructed (i.e., mock) communities.

::DEVELOPER

Caporaso Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Python

:: DOWNLOAD

Mockrobiota

:: MORE INFORMATION

Citation

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking.
Bokulich NA, Rideout JR, Mercurio WG, Shiffer A, Wolfe B, Maurice CF, Dutton RJ, Turnbaugh PJ, Knight R, Caporaso JG.
mSystems. 2016 Oct 18;1(5). pii: e00062-16

PPDbench – Benchmarking of Docking software on Protein-peptide Complexes

PPDbench

:: DESCRIPTION

PPDbench server is made in order to provide an easy webserver to calculate FNAT, L-RMSD and I-RMSD values of docked and original poses of protein-peptide complexe’s.

::DEVELOPER

PPDbench team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Benchmarking of different molecular docking methods for protein-peptide docking.
Agrawal P, Singh H, Srivastava HK, Singh S, Kishore G, Raghava GPS.
BMC Bioinformatics. 2019 Feb 4;19(Suppl 13):426. doi: 10.1186/s12859-018-2449-y.