Grape 1.1.0 – Pipeline for Processing and Analyzing RNA-Seq data

Grape 1.1.0

:: DESCRIPTION

The Grape RNAseq Analysis Pipeline Environment implements a set of workflows that allow for easy exploration of RNA-Seq data.

::DEVELOPER

Guigo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Grape

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Mar 1;29(5):614-21. doi: 10.1093/bioinformatics/btt016. Epub 2013 Jan 17.
Grape RNA-Seq analysis pipeline environment.
Knowles DG, Röder M, Merkel A, Guigó R.

flowLearn – Machine-learning algorithm for Gating Flow Cytometry data

flowLearn

:: DESCRIPTION

flowLearn is a semi-supervised approach for the quality-checked identification of cell populations.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

flowLearn

:: MORE INFORMATION

Citation

Lux M, Brinkman RR, Chauve C, Laing A, Lorenc A, Abeler-Dörner L, Hammer B.
flowLearn: fast and precise identification and quality checking of cell populations in flow cytometry.
Bioinformatics. 2018 Jul 1;34(13):2245-2253. doi: 10.1093/bioinformatics/bty082. PMID: 29462241; PMCID: PMC6022609.

singlecellVR – Interactive Visualization of Single-Cell Data in Virtual Reality

singlecellVR

:: DESCRIPTION

singlecellVR is a browser-contained, free, and open-access tool that allows users to interactively explore published studies or new data through an innovative VR interface. singlecellVR supports clustering, trajectory inference and abstract graph analysis for transcriptomic as well as epigenomic single cell data.

::DEVELOPER

Pinello Lab.

:: SCREENSHOTS

:: REQUIREMENTS

  • virtual reality hardware

:: DOWNLOAD

singlecellVR

:: MORE INFORMATION

Citation

Stein DF, Chen H, Vinyard ME, Qin Q, Combs RD, Zhang Q, Pinello L.
singlecellVR: Interactive Visualization of Single-Cell Data in Virtual Reality.
Front Genet. 2021 Oct 28;12:764170. doi: 10.3389/fgene.2021.764170. PMID: 34777482; PMCID: PMC8582280.

ESPRIT-Tree 1.2 – Hierarchical Clustering Analysis of Massive Sequence data

ESPRIT-Tree 1.2

:: DESCRIPTION

ESPRIT-Tree is a software for hierarchical clustering analysis of massive sequence data.

::DEVELOPER

Bioinformatics Laboratory, SUNY Buffalo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  ESPRIT-Tree

:: MORE INFORMATION

Citation:

Y. Cai and Y. Sun
ESPRIT-Tree: Hierarchical Clustering Analysis of Millions of 16S rRNA Pyrosequences in Quasilinear Time,
Nucleic Acids Research, vol. 39, no. 14, e95, 2011. (impact factor: 7.8)

CFinder 2.0.6 – Cluster data represented by Large Graphs

CFinder 2.0.6

:: DESCRIPTION

CFinder offers a fast and efficient method for clustering data represented by large graphs, such as genetic or social networks and microarray data. CFinder is a free software for finding overlapping dense groups of nodes in networks, based on the Clique Percolation Method, CPM, of Palla et. al. Nature (2005).

::DEVELOPER

CFinder Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java

:: DOWNLOAD

  CFinder

:: MORE INFORMATION

Citation

CFinder: locating cliques and overlapping modules in biological networks.
Adamcsek B, Palla G, Farkas IJ, Derényi I, Vicsek T.
Bioinformatics. 2006 Apr 15;22(8):1021-3. Epub 2006 Feb 10.

BIC-seq 2 0.2.4 – Copy Number analysis from Whole-genome Sequencing data

BIC-seq 2 0.2.4

:: DESCRIPTION

BIC-seq can accurately and efficiently identify CNVs via minimizing the Bayesian information criterion.Using BIC-seq, we identified hundreds of CNVs as small as 40 bp in the cancer genome sequenced at 10× coverage, whereas we could only detect large CNVs (> 15 kb) in the array comparative genomic hybridization profiles for the same genome.

::DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R package / Perl

:: DOWNLOAD

 BIC-seq

:: MORE INFORMATION

Citation

Xi et al,
Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion
PNAS, 2011 November 15, 2011 vol. 108 no. 46

chipchipnorm 1.0.1 – Normalize 2-color Microarray Data

chipchipnorm 1.0.1

:: DESCRIPTION

chipchipnorm (ChIP-chip normalization) is a R package that can be incorporated into the normalization workflow for chip-chip data, chromatin immunoprecipitation (ChIP) with microarray technology (chip).

:DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • R package

:: DOWNLOAD

 chipchipnorm

:: MORE INFORMATION

Citation

Shouyong Peng, Artyom A Alekseyenko, Erica Larschan, Mitzi I Kuroda, and Peter J Park.
Normalization and experimental design for ChIP-chip data.
BMC Bioinformatics, 8(219), 2007.

LAILAPS – Search Engine for Life Science data

LAILAPS

:: DESCRIPTION

LAILAPS combines a keyword driven search engine for an integrative access to life science databases, machine learning for a content driven relevance ranking, recommender systems for suggestion of related data records and query refinements with a user feedback tracking system for an self learning relevance training

::DEVELOPER

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 LAILAPS

:: MORE INFORMATION

Citation

M. Lange et al.
The LAILAPS Search Engine: Relevance Ranking in Life Science Databases
Journal of Integrative Bioinformatics. 7(2), 2010:

Cromwell 1.0 – The New Model Processor for Mass Spectrometry Data

Cromwell 1.0

:: DESCRIPTION

Cromwell is an implementation of our algorithms for low-level processing of mass spectrometry proteomics data. Cromwell represents our third attempt (at least) to find a method to process spectra that both works quickly and achieves reasonably good results.

::DEVELOPER

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab

:: DOWNLOAD

 Cromwell

:: MORE INFORMATION

Citation

Cancer Inform. 2005;1:41-52.
Understanding the characteristics of mass spectrometry data through the use of simulation.
Coombes KR, Koomen JM, Baggerly KA, Morris JS, Kobayashi R.

GenEx 7.0 – Analyze Real-time qPCR Data

GenEx 7.0

:: DESCRIPTION

GenEx is a popular software for qPCR data processing and analysis. Built in a modular fashion GenEx provides a multitude of functionalities for the qPCR community, ranging from basic data editing and management to advanced cutting-edge data analysis.

::DEVELOPER

MultiD Analyses AB

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  GenEx

:: MORE INFORMATION