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http://www.sysbio.se/piano/

Software R-package for running gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. The Piano package contains functions for combining the results of multiple runs of gene set analyses.

Proper citation: Piano (RRID:SCR_003200) Copy   

•   Source: SciCrunch Registry

http://cmb.molgen.mpg.de/2ndGenerationSequencing/Solas/

Software package for the statistical language R, devoted to the analysis of next generation short read data of RNA-seq transcripts. It provides predictions of alternative exons in a single condition/cell sample, predictions of differential alternative exons between two conditions/cell samples, and quantification of alternative splice forms in a single condition/cell sample.

Proper citation: Solas (RRID:SCR_003168) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/cancer/software/genepattern

A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.

Proper citation: GenePattern (RRID:SCR_003201) Copy   

•   Source: SciCrunch Registry

http://pir.georgetown.edu/pirwww/dbinfo/pirsf.shtml

A SuperFamily classification system, with rules for functional site and protein name, to facilitate the sensible propagation and standardization of protein annotation and the systematic detection of annotation errors. The PIRSF concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. The PIRSF classification system is based on whole proteins rather than on the component domains; therefore, it allows annotation of generic biochemical and specific biological functions, as well as classification of proteins without well-defined domains. There are different PIRSF classification levels. The primary level is the homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture). At a lower level are the subfamilies which are clusters representing functional specialization and/or domain architecture variation within the family. Above the homeomorphic level there may be parent superfamilies that connect distantly related families and orphan proteins based on common domains. Because proteins can belong to more than one domain superfamily, the PIRSF structure is formally a network. The FTP site provides free download for PIRSF.

Proper citation: PIRSF (RRID:SCR_003352) Copy   

•   Source: SciCrunch Registry

https://github.com/ggloor/ALDEx2

Software tool to examine compositional high-throughput sequence data with Welch's t-test. A differential relative count abundance analysis for the comparison of two conditions. For example, single-organism and meta-rna-seq high-throughput sequencing assays, or of selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected Benjamini-Hochberg false discovery rate given the biological and sampling variation using several parametric and non-parametric tests. Can to glm and Kruskal-Wallace tests on one-way ANOVA style designs.

Proper citation: ALDEx2 (RRID:SCR_003364) Copy   

•   Source: SciCrunch Registry

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

An R package for extending the grammar of graphics for genomic data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.

Proper citation: ggbio (RRID:SCR_003313) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/dranew/defuse

Software package for gene fusion discovery using RNA-Seq data. It uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries.

Proper citation: deFuse (RRID:SCR_003279) Copy   

•   Source: SciCrunch Registry

http://primerseq.sourceforge.net/

Software that designs RT-PCR primers that evaluate alternative splicing events by incorporating RNA-Seq data. It is particularly advantageous for designing a large number of primers for validating alternative splicing events found in RNA-Seq data. It incorporates RNA-Seq data in the design process to weight exons by their read counts. Essentially, the RNA-Seq data allows primers to be placed using actually expressed transcripts. This could be for a particular cell line or experimental condition, rather than using annotations that incorporate transcripts that are not expressed for the data. Alternatively, you can design primers that are always on constitutive exons. PrimerSeq does not limit the use of gene annotations and can be used for a wide array of species.

Proper citation: PrimerSeq (RRID:SCR_003295) Copy   

•   Source: SciCrunch Registry

http://shendurelab.github.io/MIPGEN/

Software for a fast, simple way to generate designs for MIP assays targeting hundreds or thousands of genomic loci in parallel. Packaged with MIPgen are scripts that aid in visualization of MIP designs and processing of MIP sequence reads to SAM files that can then be passed through any standard variant calling pipeline.

Proper citation: MIPgen (RRID:SCR_003325) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/johanneskoester/snakemake/wiki/

A Python based language and execution environment for make-like workflows. The system supports the use of automatically inferred multiple named wildcards (or variables) in input and output filenames.

Proper citation: Snakemake (RRID:SCR_003475) Copy   

•   Source: SciCrunch Registry

http://knowledgemap.mc.vanderbilt.edu/research/content/phewas-r-package

Software package contains methods for performing Phenome-Wide Association Study.

Proper citation: PheWAS R Package (RRID:SCR_003512) Copy   

•   Source: SciCrunch Registry

http://www.cellimagelibrary.org/

Freely accessible, public repository of vetted and annotated microscopic images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. Explore by Cell Process, Cell Component, Cell Type or Organism. The Cell includes images acquired from historical and modern collections, publications, and by recruitment.

Proper citation: Cell Image Library (CIL) (RRID:SCR_003510) Copy   

•   Source: SciCrunch Registry

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

Software tool for running and managing bioinformatics pipelines. It specializes in enabling users to turn existing pipelines based on shell scripts or command line tools into highly flexible, adaptable and maintainable workflows with a minimum of effort. Bpipe ensures that pipelines execute in a controlled and repeatable fashion and keeps audit trails and logs to ensure that experimental results are reproducible. Requiring only Java as a dependency, it is fully self-contained and cross-platform, making it very easy to adopt and deploy into existing environments.

Proper citation: Bpipe (RRID:SCR_003471) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/pride/

Centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. Originally it was developed to provide a common data exchange format and repository to support proteomics literature publications. This remit has grown with PRIDE, with the hope that PRIDE will provide a reference set of tissue-based identifications for use by the community. The future development of PRIDE has become closely linked to HUPO PSI. PRIDE encourages and welcomes direct user submissions of protein and peptide identification data to be published in peer-reviewed publications. Users may Browse public datasets, use PRIDE BioMart for custom queries, or download the data directly from the FTP site. PRIDE has been developed through a collaboration of the EMBL-EBI, Ghent University in Belgium, and the University of Manchester.

Proper citation: Proteomics Identifications (PRIDE) (RRID:SCR_003411) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.biostat.wisc.edu/~kendzior/EBSEQ/

Software R package for RNA-Seq Differential Expression Analysis.

Proper citation: EBSeq (RRID:SCR_003526) Copy   

•   Source: SciCrunch Registry

http://www.reactome.org

Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets.

Proper citation: Reactome (RRID:SCR_003485) Copy   

•   Source: SciCrunch Registry

http://cng.gmu.edu:8080/Lm

A freely available software tool available for the Windows and Linux platform, as well as the Online version Applet, for the analysis, comparison and search of digital reconstructions of neuronal morphologies. For the quantitative characterization of neuronal morphology, LM computes a large number of neuroanatomical parameters from 3D digital reconstruction files starting from and combining a set of core metrics. After more than six years of development and use in the neuroscience community, LM enables the execution of commonly adopted analyses as well as of more advanced functions, including: (i) extraction of basic morphological parameters, (ii) computation of frequency distributions, (iii) measurements from user-specified subregions of the neuronal arbors, (iv) statistical comparison between two groups of cells and (v) filtered selections and searches from collections of neurons based on any Boolean combination of the available morphometric measures. These functionalities are easily accessed and deployed through a user-friendly graphical interface and typically execute within few minutes on a set of 20 neurons. The tool is available for either online use on any Java-enabled browser and platform or may be downloaded for local execution under Windows and Linux.

Proper citation: L-Measure (RRID:SCR_003487) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry