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http://brainarray.mbni.med.umich.edu/Brainarray/Database/SearchSNP/snpfunc.aspx

Database for exploring the function implication of single nucleotide polymorphism (SNP) alleles. It is designed to be a clearing house for all public domain SNP functional annotation data, as well as in-house functional annotations derived from different data sources. It currently contains SNP functional annotations in six major categories including genomic elements, transcription regulation, protein function, pathway, disease and population genetics. Besides extensive SNP functional annotations, it includes a search engine that accepts different types of genetic markers as input and identifies all genetically related SNPs based on the HapMap Phase II data as well as the relationship of different markers to known genes. As a result, the system allows users to identify the potential biological impact of genetic markers and complex relationships among genetic markers and genes, and it greatly facilitates knowledge discovery in genome-wide SNP scanning experiments.

Proper citation: SNP Function Portal (RRID:SCR_001954) Copy   

•   Source: SciCrunch Registry

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

Software for phenotyping Flow Cytometry assays using multidimentional expansion of single dimentional partitions.

Proper citation: flowType (RRID:SCR_001957) Copy   

•   Source: SciCrunch Registry

http://www.cs.sunysb.edu/~skiena/shorty/

Software for targeted de novo assembly of microreads with mate pair information and sequencing errors.

Proper citation: SHORTY (RRID:SCR_002048) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/ADaCGH2.html

Software for analysis and plotting of array comparative genomic hybridization (CGH) data. It allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.

Proper citation: ADaCGH2 (RRID:SCR_001981) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/src/contrib/Archive/PurBayes/

An MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data.

Proper citation: PurBayes (RRID:SCR_002068) Copy   

•   Source: SciCrunch Registry

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

Software providing a HTML5/javascript based browser for visualizing RNA-seq results in the familiar track layout of common genome browser. But given the quantitative nature of RNA-seq data, in addition to visualizing sequence coverage, the browser quantitates transcript abundance across regions of interest. The HTML5 functionality is made of use to render all the tracks using the canvas drawing element. This greatly reduces the load on servers and allows for rich interactive graphics without the need for third-party plugins. Furthermore, this framework completely segregates data from visualization, making development much easier. The browser is designed to run on all modern browsers: Firefox, Safari, Chrome, Opera and Internet Explorer (though not recommended).

Proper citation: tbrowse (RRID:SCR_001918) Copy   

•   Source: SciCrunch Registry

http://microarrays.curie.fr/publications/U900-RPPA_PLT/Normacurve/

Analysis methodology that allows simultaneous quantification and normalization of reverse phase protein array (RPPA) data.

Proper citation: NormaCurve (RRID:SCR_001995) Copy   

•   Source: SciCrunch Registry

https://github.com/xflouris/gapmis

A software tool for pairwise sequence alignment with a single gap.

Proper citation: GapMis (RRID:SCR_001999) Copy   

•   Source: SciCrunch Registry

http://figshare.com/articles/Tool_for_rapid_annotation_of_microbial_SNPs_TRAMS_a_simple_program_for_rapid_annotation_of_genomic_variation_in_prokaryotes_/782261

A software program for functional annotation of genomic single nucleotide polymorphisms (SNPs) which is available to download as a single file executable for WINDOWS users with limited computational experience and as a Python script for Mac OS and Linux users. It needs only a tab delimited text file containing SNP locations, reference nucleotide and SNPs in different strains along with a reference genome sequence in standard GenBank or EMBL format. It annotates SNPs as synonymous, non-synonymous or nonsense. Non-synonymous SNPs in start and stop codons are separated as non-start and non-stop SNPs, respectively. SNPs in overlapping features are annotated separately for each feature and multiple nucleotide polymorphisms (MNPs) within a codon are combined prior to annotation. A workflow has also been developed for use in Galaxy to map short reads to a reference genome and extract and annotate the SNPs.

Proper citation: TRAMS (RRID:SCR_002003) Copy   

•   Source: SciCrunch Registry

http://drpowell.github.io/vennt/

A web-tool to generate dynamic Venn diagrams for differential gene expression.

Proper citation: Vennt (RRID:SCR_002083) Copy   

•   Source: SciCrunch Registry

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

An R/Bioconductor package for quality assessment of target enrichment experiments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on.

Proper citation: TEQC (RRID:SCR_001943) Copy   

•   Source: SciCrunch Registry

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

Software that provides visualization tools for flow cytometry data.

Proper citation: flowViz (RRID:SCR_002075) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.11/bioc/html/flowQB.html

A fully automated R Bioconductor package to calculate automatically the detector efficiency (Q), optical background (B) and intrinsic CV of the beads.

Proper citation: flowQB (RRID:SCR_002144) Copy   

•   Source: SciCrunch Registry

http://amigo.geneontology.org/

Web tool to search, sort, analyze, visualize and download data of interest. Along with providing details of the ontologies, gene products and annotations, features a BLAST search, Term Enrichment and GO Slimmer tools, the GO Online SQL Environment and a user help guide.Used at the Gene Ontology (GO) website to access the data provided by the GO Consortium. Developed and maintained by the GO Consortium.

Proper citation: AmiGO (RRID:SCR_002143) Copy   

•   Source: SciCrunch Registry

http://cinteny.cchmc.org/

Online database for finding and analyzing syntenic regions across multiple genomes and measuring the extent of genome rearrangement using reversal distance as a measure.

Proper citation: Cinteny (RRID:SCR_002147) Copy   

•   Source: SciCrunch Registry

https://github.com/TGAC/miso-lims

Open source software for a Laboratory Information Management System (LIMS) for NGS sequencing centres.

Proper citation: miso-lims (RRID:SCR_002259) Copy   

•   Source: SciCrunch Registry

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

A Bioconductor package designed to perform quantitative analysis of cell proliferation in tracking dye-based experiments. The package uses an R implementation of the Levenberg-Marquardt algorithm (minpack.lm) to fit a set of peaks (corresponding to different generations of cells) over the proliferation-tracking dye distribution in a FACS experiment.

Proper citation: flowFit (RRID:SCR_002286) Copy   

•   Source: SciCrunch Registry

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

An easy-to-use R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.

Proper citation: spliceR (RRID:SCR_002280) Copy   

•   Source: SciCrunch Registry

http://insulatordb.uthsc.edu/

A comprehensive collection of experimentally determined and computationally predicted CCCTC-binding factor (CTCF) binding sites (CTCFBS) from the literature. The database is designed to facilitate the studies on insulators and their roles in demarcating functional genomic domains. The CTCFBS Prediction Tool allows users to scan sequences for the single best match to CTCF position weight matrices. Currently (March 2014), the database contains almost 15 million experimentally determined CTCF binding sites across several species. CTCF binding sites were collected from published papers containing CTCF binding sites identified using ChIPSeq or similar methods, data from the ENCODE project, and a set of approximately 100 manually curated binding sites identified by low-throughput experiments. Users can browse insulator sequence features, function annotations, genomic contexts including histone methylation profiles, flanking gene expression patterns and orthologous regions in other mammalian genomes. Users can also retrieve data by text search, sequence search and genomic range search.

Proper citation: CTCFBSDB (RRID:SCR_002279) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/frhit/

An efficient fragment recruitment software program for next generation sequences against microbial reference genomes. It produces similar sensitivity of BLASTN, but runs at a 100 times higher speed. The algorithm adopts a seeding heuristic strategy with overlapping k-mer hashing to locate candidate matching blocks on the reference sequences, and then apply an effective filtering within the candidate blocks to filter out blocks that do not meet the minimum criteria for containing an alignment with specified parameters. For each candidate block that passed the filter, the best matching sub-regions between a candidate block and a read are determined, and used subsequently by the banded Smith-Waterman algorithm to carry out the actual alignment efficiently, which will finally verify if this can be a valid recruitment hit.

Proper citation: FR-HIT (RRID:SCR_002181) Copy   

•   Source: SciCrunch Registry