Abacus 20160720 – Extracting Spectral Counts from MS/MS Data Sets.

Abacus 20160720

:: DESCRIPTION

Abacus is a tool for extracting adjusted spectral counts from the result XML files generated by the Trans-Proteomic Pipeline (TPP). Abacus outputs a tab-delimited file that can be used for label-free quantification or simply viewing proteomics results across multiple experimental runs.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOs
  • Java

:: DOWNLOAD

Abacus 

:: MORE INFORMATION

Citation:

Proteomics. 2011 Apr;11(7):1340-5. doi: 10.1002/pmic.201000650. Epub 2011 Feb 17.
Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis.
Fermin D, Basrur V, Yocum AK, Nesvizhskii AI.

EPIG-Seq v1.0 – Extracting Patterns and Identifying co-expressed Genes from RNA-Seq

EPIG-Seq v1.0

:: DESCRIPTION

EPIG-Seq is an algorithm and software to identify gene expression patterns from RNA-Seq count data. Once the patterns are identified, co-expressed genes are clustered to the patterns.

::DEVELOPER

EPIG-Seq team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

EPIG-Seq

:: MORE INFORMATION

Citation:

BMC Genomics. 2016 Mar 22;17:255. doi: 10.1186/s12864-016-2584-7.
EPIG-Seq: extracting patterns and identifying co-expressed genes from RNA-Seq data.
Li J, Bushel PR.

SICLE 1.2 – high-throughput tool for Extracting Evolutionary Relationships from Phylogenetic Trees

SICLE 1.2

:: DESCRIPTION

SICLE (Sister Clade Extractor) is an easy to use, adaptable, and high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship.

::DEVELOPER

Dr. Dan DeBlasio

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 SICLE

:: MORE INFORMATION

Citation

SICLE: A high-throughput tool for extracting evolutionary relationships from phylogenetic trees
Dan DeBlasio, Jennifer Wiscaver
Genomics arXiv:1303.5785

GEO2Enrichr – Browser Extension for Extracting Differentially Expressed Gene Sets from GEO

GEO2Enrichr

:: DESCRIPTION

GEO2Enrichr is web application and two browser extensions (one for Chrome and another for Firefox) designed to facilitate the extraction of signatures from studies posted on the Gene Expression Omnibus (GEO) database.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Chrome / Firefox

:: DOWNLOAD

GEO2Enrichr

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Sep 15;31(18):3060-2. doi: 10.1093/bioinformatics/btv297. Epub 2015 May 13.
GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions.
Gundersen GW, Jones MR, Rouillard AD, Kou Y, Monteiro CD, Feldmann AS, Hu KS, Ma’ayan A.

Rna3Dmotif – Software for Extracting RNA Tertiary Motifs

Rna3Dmotif

:: DESCRIPTION

Rna3Dmotif is a free bundle of three easy-to-install programs aimed to be used in combination to automatically extract recurrent RNA local tertiary motifs. The approach used is based on a graph representation of the RNA tertiary structure using LW no-menclature. It was applied to three widely studied ribosomal RNA structures and the motifs thus found were deposited in a dedicated repository.

::DEVELOPER

Mahassine Djelloul

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Rna3Dmotif

:: MORE INFORMATION

ASprofile – Extracting, Quantifying and Comparing Alternative Splicing (AS) Events from RNA-seq data

ASprofile

:: DESCRIPTION

ASprofile is a suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data.

::DEVELOPER

Center for Computational Biology , Johns Hopkins University School of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  ASprofile

:: MORE INFORMATION