:: DESCRIPTION
The Grape RNAseq Analysis Pipeline Environment implements a set of workflows that allow for easy exploration of RNA-Seq data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
ESPRIT-Tree is a software for hierarchical clustering analysis of massive sequence data.
::DEVELOPER
Bioinformatics Laboratory, SUNY Buffalo
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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)
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: MORE INFORMATION
Citation
M. Lange et al.
The LAILAPS Search Engine: Relevance Ranking in Life Science Databases
Journal of Integrative Bioinformatics. 7(2), 2010:
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
