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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://cbio.mskcc.org/public/raetschlab/user/drewe/rdiff/

Software tool for detecting differential RNA processing from RNA-Seq data. It implements two statistical tests, rDiff.parametric and rDiff.nonparametric, to detect changes of the RNA processing between two samples.

Proper citation: rDiff (RRID:SCR_003162) 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

http://mouseNET.princeton.edu

A functional network for laboratory mouse based on integration of diverse genetic and genomic data. It allows the users to accurately predict novel functional assignments and network components. MouseNET uses a probabilistic Bayesian algorithm to identify genes that are most likely to be in the same pathway/functional neighborhood as your genes of interest. It then displays biological network for the resulting genes as a graph. The nodes in the graph are genes (clicking on each node will bring up SGD page for that gene) and edges are interactions (clicking on each edge will show evidence used to predict this interaction). Most likely, the first results to load on the results page will be a list of significant Gene Ontology terms. This list is calculated for the genes in the biological network created by the mouseNET algorithm. If a gene ontology term appears on this list with a low p-value, it is statistically significantly overrepresented in this biological network. The graph may be explored further. As you move the mouse over genes in the network, interactions involving these genes are highlighted.If you click on any of the highlighted interactions graph, evidence pop-up window will appear. The Evidence pop-up lists all evidence for this interaction, with links to the papers that produced this evidence - clicking these links will bring up the relevant source citation(s) in PubMed.

Proper citation: MouseNET (RRID:SCR_003357) 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://cran.r-project.org/web/packages/RCircos/

Software package that provides a simple and flexible way to generate Circos 2D track plot images for genomic data visualization. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics package that comes with R base installation.

Proper citation: RCircos (RRID:SCR_003310) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/primerdesigner/

High throughput PCR primer design software. Target regions defined through a rich set of descriptors, such as Ensembl accessions and arbitrary genomic coordinates, may be specified. Primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the specified target regions. As part of the tiling process, primer pairs are computationally screened to meet the criteria for success with one of two PCR amplification protocols.

Proper citation: JCVI Primer Designer (RRID:SCR_003275) Copy   

•   Source: SciCrunch Registry

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

Software package providing an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. It requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The package implements a pipeline to collect, analyze and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions.

Proper citation: ddCt (RRID:SCR_003396) 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://moma.dk/normfinder-software

Software for identifying the optimal normalization gene among a set of candidates. It ranks the set of candidate normalization genes according to their expression stability in a given sample set and given experimental design. It can analyze expression data obtained through any quantitative method e.g. real time RT-PCR and microarray based expression analysis. NormFinder.xla adds the NormFinder functionality directly to Excel. A version for R is also available.

Proper citation: NormFinder (RRID:SCR_003387) Copy   

•   Source: SciCrunch Registry

http://www.genedata.com/products/expressionist/genomic-profiling.html

Software that provides data processing, analysis, management, and reporting of metabolomics, proteomics and biotherapeutics characterization studies based on mass spectrometry. It can process raw data from various MS instruments, serve MS processing, analysis and reporting needs, and ensure reproducibility and traceability of results.

Proper citation: Genedata Expressionist (RRID:SCR_003298) 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://www.bioconductor.org/packages/devel/bioc/html/OmicCircos.html

An R software application and package used to generate high-quality circular plots for visualizing genomic variations, including mutation patterns, copy number variations (CNVs), expression patterns, and methylation patterns.

Proper citation: OmicCircos (RRID:SCR_003292) 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://code.google.com/p/popoolation2/

Software to compare allele frequencies for SNPs between two or more populations and to identify significant differences. PoPoolation2 requires next generation sequencing data of pooled genomic DNA (Pool-Seq). It may be used for measuring differentiation between populations, for genome wide association studies and for experimental evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PoPoolation2 (RRID:SCR_003284) Copy   

•   Source: SciCrunch Registry

https://github.com/outbig/DAFGA

A python script package which estimates the evolutionary rate of a particular functional gene in a standardized manner by relating its sequence divergence to that of the 16S rRNA gene. It provides gene-specific parameter sets for OTU clustering and taxonomic assignment at desired rank, and it can be implemented into the diversity measurements offered by QIIME or Mothur.

Proper citation: DAFGA (RRID:SCR_003319) 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

https://github.com/BauerLab/ngsane

Software providing a Linux-based High Performance Computing (HPC) enabled framework for high-throughput data analysis that minimizes overhead for set up and processing of new projects yet maintains full flexibility of custom scripting when processing raw sequence data.

Proper citation: NGSANE (RRID:SCR_003478) Copy   

•   Source: SciCrunch Registry