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http://www.bioconductor.org/packages/release/bioc/html/aroma.light.html

Light-weight software package for normalization and visualization of microarray data using only basic R data types. Software can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.

Proper citation: aroma.light (RRID:SCR_001312) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.13/bioc/html/BeadDataPackR.html

Software that provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform.

Proper citation: BeadDataPackR (RRID:SCR_001310) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/bioc/html/OLIN.html

Software functions for normalization of two-color microarrays by optimised local regression and for detection of artifacts in microarray data.

Proper citation: OLIN (RRID:SCR_001304) Copy   

•   Source: SciCrunch Registry

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

Software package that provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats.

Proper citation: qcmetrics (RRID:SCR_001303) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.12/bioc/html/dexus.html

Software package that identifies differentially expressed genes in RNA-Seq data under all possible study designs such as studies without replicates, without sample groups, and with unknown conditions. It works also for known conditions, for example for RNA-Seq data with two or multiple conditions. RNA-Seq read count data can be provided both by the S4 class Count Data Set and by read count matrices. Differentially expressed transcripts can be visualized by heatmaps, in which unknown conditions, replicates, and samples groups are also indicated. This software is fast since the core algorithm is written in C. For very large data sets, a parallel version of DEXUS is provided in this package. DEXUS is a statistical model that is selected in a Bayesian framework by an EM algorithm. It does not need replicates to detect differentially expressed transcripts, since the replicates (or conditions) are estimated by the EM method for each transcript. The method provides an informative/non-informative value to extract differentially expressed transcripts at a desired significance level or power.

Proper citation: DEXUS (RRID:SCR_001309) Copy   

•   Source: SciCrunch Registry

http://mugsy.sourceforge.net/

Software resource for multiple whole genome alignment. It uses Nucmer, a custom graph-based segmentation procedure, for pairwise alignment, and the Seqan:TCoffee's multiple alignment strategy.

Proper citation: Mugsy (RRID:SCR_001414) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/cell-motility/

An open source Java application that provides a clear and concise analysis workbench for large amounts of cell motion data.

Proper citation: Cell motility (RRID:SCR_012120) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/isdtool/files/ISDTool-2.0/

Software that implements a computational model for predicting immunosuppressive domains (ISDs). The software could be used to identify typical ISDs in retroviruses including HERV, HTLV, HIV, STLV, SIV and MLV.

Proper citation: ISDTool (RRID:SCR_012125) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngopt/

Software that produces high quality microbial genome assemblies on a laptop computer without any parameter tuning. A5-miseq does this by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation, and detection of misassemblies. Unlike the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing information during contig generation, and includes several improvements to read trimming.

Proper citation: A5-miseq (RRID:SCR_012148) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/plek/

An alignment-free software tool which uses a computational pipeline based on an improved k-mer scheme and a support vector machine (SVM) algorithm to distinguish lncRNAs from messenger RNAs (mRNAs), in the absence of genomic sequences or annotations. It is especially suitable for PacBio or 454 sequencing data and large-scale transcriptome data.

Proper citation: PLEK (RRID:SCR_012132) Copy   

•   Source: SciCrunch Registry

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

A suite of python scripts to perform high-throughput investigation of RNA editing using next-generation sequencing data.

Proper citation: REDItools (RRID:SCR_012133) Copy   

•   Source: SciCrunch Registry

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

Software that builds on probability theory to visualize significant conserved sequence patterns in multiple peptide sequence alignments against background (reference) sequence sets that can be tailored to the studied system and the used protocol.

Proper citation: iceLogo (RRID:SCR_012137) Copy   

•   Source: SciCrunch Registry

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

Software that predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences. The source code and precompiled binaries of brainstorming tool are available under Apache licensing.

Proper citation: AMS (RRID:SCR_012140) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/phosphosite/

A bioinformatical software tool for analyzing (quantitative) phosphoproteome datasets. The program retrieves kinase-substrate predictions from NetworKIN and contains various statistical modules for futher analysis.

Proper citation: PhosphoSiteAnalyzer (RRID:SCR_012142) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/DNAcopy.html

Software that segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number.

Proper citation: DNAcopy (RRID:SCR_012560) Copy   

•   Source: SciCrunch Registry

http://autodock.scripps.edu/

Software suite of automated docking tools. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure. AutoDock consist of AutoDock 4 and AutoDock Vina. AutoDock 4 consists of autodock to perform docking of ligand to set of grids describing target protein, and autogrid to pre calculate these grids.

Proper citation: AutoDock (RRID:SCR_012746) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/edgeR/

Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.

Proper citation: edgeR (RRID:SCR_012802) Copy   

•   Source: SciCrunch Registry

http://www.imgt.org/

A high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MHC superfamily (MhcSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates, serving as the global reference in immunogenetics and immunoinformatics. IMGT provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools.

Proper citation: IMGT - the international ImMunoGeneTics information system (RRID:SCR_012780) Copy   

•   Source: SciCrunch Registry

https://github.com/bedops/bedops

A suite of tools to address common questions raised in genomic studies - mostly with regard to overlap and proximity relationships between data sets.

Proper citation: BEDOPS (RRID:SCR_012865) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/featureCounts/

A read summarization program, which counts mapped reads for the genomic features such as genes and exons.

Proper citation: featureCounts (RRID:SCR_012919) Copy   

•   Source: SciCrunch Registry