:: DESCRIPTION
degPrune is a program for pruning most non-differentially expressed genes from microarray data in PCL or NCBI GEO format
::DEVELOPER
Machine Learning and Evolution Laboratory (MLEG)
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: MORE INFORMATION
Citation:
BMC Genomics. 2010 Nov 2;11 Suppl 2:S3. doi: 10.1186/1471-2164-11-S2-S3.
Density based pruning for identification of differentially expressed genes from microarray data.
Hu J1, Xu J.
:: DESCRIPTION
The purpose of sSeq is to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation. The method of moment (MM) estimates for dispersion are shrunk towards an estimated target, which minimizes the average squared difference between the shrinkage estimates and the initial estimates. The exact per-gene probability under the NB model is calculated, and used to test the hypothesis that the expected expression of a gene in two conditions identically follow a NB distribution.
::DEVELOPER
Laboratory for Statistical Proteomics and Bioinformatics , Purdue University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 May 15;29(10):1275-82. doi: 10.1093/bioinformatics/btt143. Epub 2013 Apr 14.
Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size.
Yu D, Huber W, Vitek O.
