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http://mrbayes.sourceforge.net/

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 28,2023. Software program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.

Proper citation: MrBayes (RRID:SCR_012067) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/open-ms/

An algorithm to align LC-MS samples and to match corresponding ion species across samples.

Proper citation: OpenMS (RRID:SCR_012042) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/pegasus-fus/

Software that annotates biologically functional gene fusion candidates.

Proper citation: Pegasus-fus (RRID:SCR_012118) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/nailsystemsbiology/

A set of software tools to simplify the range of computational activities involved in regulatory network inference. It is technology-independent and includes an interface layer to allow easy integration of components into other applications. It is implemented in MATLAB and is available for all researchers to use.

Proper citation: NAIL (RRID:SCR_012134) Copy   

•   Source: SciCrunch Registry

http://xmsanalyzer.sourceforge.net

A software package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. xMSanalyzer comprises of utilities that can be classified into five main modules: 1) merging apLCMS or XCMS sample processing results from multiple sets of parameter settings, 2) evaluation of sample quality, feature consistency, and batch-effect, 3) feature matching, and 4) characterization of m/z using KEGG REST; 5) Batch-effect correction using ComBat.

Proper citation: xMSanalyzer (RRID:SCR_012144) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/heuraa/

Software for accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.

Proper citation: HeurAA (RRID:SCR_013212) Copy   

•   Source: SciCrunch Registry

http://facil-host.cmbi.umcn.nl/facil

Genetic code prediction tool that infers the genetic code directly from any set of nucleic acid sequences and assigns a Random Forest-based reliability score to its predictions.

Proper citation: FACIL (RRID:SCR_004375) Copy   

•   Source: SciCrunch Registry

http://www.mathcs.emory.edu/panda/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Web-based software program for analyzing phosphorylation antibody arrays. It identifies phosphorylated antibodies in the microarray and statistically quantifies the extent of phosphorylation for these antibodies.

Proper citation: Phosphor Antibody Array Data Analysis (RRID:SCR_000633) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/iontree.html

Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry.

Proper citation: iontree (RRID:SCR_002813) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/devel/bioc/html/RUVSeq.html

Software package that implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.

Proper citation: RUVSeq (RRID:SCR_006263) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/reseqtools/

A Toolkit for analyzing next-generation DNA Re-Sequencing data.

Proper citation: reseqtools (RRID:SCR_010806) Copy   

•   Source: SciCrunch Registry

https://github.com/neufeld/pandaseq

Software program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

Proper citation: PANDAseq (RRID:SCR_002705) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/ReadqPCR.html

A software package that provides functions to read raw RT-qPCR data of different platforms.

Proper citation: ReadqPCR (RRID:SCR_000030) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/ncdfFlow.html

Software package that provides netCDF storage based methods and functions for manipulation of flow cytometry data.

Proper citation: ncdfFlow (RRID:SCR_000009) Copy   

•   Source: SciCrunch Registry