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http://www.lgm.upmc.fr/parseq/
Statistical software for transcription landscape reconstruction at a basepair resolution from RNA Seq read counts. It is based on a state-space model which describes, in terms of abrupt shifts and more progressive drifts, the transcription level dynamics along the genome. Alongside variations of transcription level, it incorporates a component of short-range variation to pull apart local artifacts causing correlated dispersion. Reconstruction of the transcription level relies on a conditional sequential Monte Carlo approach that is combined with parameter estimation in a Markov chain Monte Carlo algorithm known as particle Gibbs. The method allows to estimate the local transcription level, to call transcribed regions, and to identify the transcript borders.
Proper citation: Parseq (RRID:SCR_003464) Copy
http://cran.r-project.org/web/packages/MultiPhen/
Software package that performs genetic association tests between SNPs (one-at-a-time) and multiple phenotypes (separately or in joint model).
Proper citation: MultiPhen (RRID:SCR_003498) Copy
http://www.biostat.wisc.edu/~kendzior/EBSEQ/
Software R package for RNA-Seq Differential Expression Analysis.
Proper citation: EBSeq (RRID:SCR_003526) Copy
https://code.google.com/p/mztab/
A Java interface to the mzTab data exchange format for reporting a summary of proteomics results.
Proper citation: jmzTab (RRID:SCR_003481) Copy
http://www.compgen.org/tools/metagen
Software program providing a method for meta-analysis of case-control genetic association studies using random-effects logistic regression.
Proper citation: metagen (RRID:SCR_003443) Copy
http://genome.sph.umich.edu/wiki/RAREMETAL
A software program that facilitates the meta-analysis of rare variants from genotype arrays or sequencing.
Proper citation: RAREMETAL (RRID:SCR_003573) Copy
https://code.google.com/p/guardd/
MATLAB software designed to organize, automate, and enhance the analytical procedures which operate on CPMG RD NMR data.
Proper citation: GUARDD (RRID:SCR_000040) Copy
https://github.com/SciLifeLab/facs
Software for classification of Sequences using Bloom filters that can accurately and rapidly align sequences to a reference sequence.
Proper citation: FACS (RRID:SCR_000055) Copy
http://www.bioconductor.org/packages/release/bioc/html/GEOquery.html
Software that establishes a bridge between GEO and BioConductor.
Proper citation: GEOquery (RRID:SCR_000146) Copy
http://sourceforge.net/projects/gemsim/
A software package for generating realistic simulated next-generation genome sequencing reads with quality score values. The software is written in Python with a command-line user interface.
Proper citation: GemSIM (RRID:SCR_000167) Copy
http://www.bioconductor.org/packages/release/bioc/html/MIMOSA.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for modeling count data using Dirichlet-multinomial and beta-binomial mixtures with applications to single-cell assays.
Proper citation: MIMOSA (RRID:SCR_000184) Copy
http://acgt.cs.tau.ac.il/modent/
A computational tool that reconstructs gene regulatory networks from high throughput experimental data.
Proper citation: MODENT - A Tool For Reconstructing Gene Regulatory Networks (RRID:SCR_000220) Copy
https://github.com/vahuynh/dynGENIE3
An algorithm for the inference of gene regulatory networks from expression data.
Proper citation: GENIE3 (RRID:SCR_000217) Copy
http://www.uniklinikum-saarland.de/einrichtungen/fachrichtungen/humangenetik/software/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software tool for predicting granzyme B and caspase cleavage sites.
Proper citation: GraBCas (RRID:SCR_000205) Copy
http://ribopicker.sourceforge.net/
Software to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets.
Proper citation: riboPicker (RRID:SCR_000360) Copy
A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads.
Proper citation: ARACHNE (RRID:SCR_000351) Copy
https://sites.google.com/site/beckerjeremie/home/nucleofinder
A software for a statistical approach for the detection of nucleosome positions in a cell population. The software identifies important features of nucleosome organization such as the spacing downstream of active promoters and the enrichment and depletion of GC/AT dinucleotides of in vitro nucleosomes.
Proper citation: NucleoFinder (RRID:SCR_000368) Copy
https://github.com/yongchao/flowPeaks
Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.
Proper citation: flowPeaks (RRID:SCR_000407) Copy
http://proteinprophet.sourceforge.net/
Software that automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST.
Proper citation: ProteinProphet (RRID:SCR_000286) Copy
Software tool for association study of high-dimensional microRNA expression data with repeated measures. The penalized regression model incorporates a grid search method for analyzing associations of high-dimensional microRNA expression data with repeated measures.
Proper citation: PGS (RRID:SCR_000475) Copy
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