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http://www.sanger.ac.uk/resources/software/artemis/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Free genome browser and annotation tool that allows visualization of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Artemis is free software and is distributed under the terms of the GNU General Public License. Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.

Proper citation: Artemis: Genome Browser and Annotation Tool (RRID:SCR_004267) Copy   

•   Source: SciCrunch Registry

http://www.ccmp.ox.ac.uk/peakdeck

A peak-calling software program for DNAseI-seq data.

Proper citation: PeaKDEck (RRID:SCR_004268) Copy   

•   Source: SciCrunch Registry

https://github.com/alyssafrazee/derfinder

R package for differential expression analysis of RNA-seq data.

Proper citation: DER Finder (RRID:SCR_004250) Copy   

•   Source: SciCrunch Registry

http://ftp://lausanne.isb-sib.ch/pub/databases/Bgee/general/IQRray.R

Software based on evolutionary conservation of expression profiles, implemented in R, for identification of poor quality arrays in dataset composed of arrays from many independent experiments.

Proper citation: IQRray (RRID:SCR_006057) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/YuGene/

Software providing a simple method for comparison of gene expression generated across different experiments, and on different platforms; that does not require global renormalization, and is not restricted to comparison of identical probes. YuGene works on a range of microarray dataset distributions, such as between manufacturers. The resulting output allows direct comparisons of gene expression between experiments and experimental platforms.

Proper citation: YuGene (RRID:SCR_006023) Copy   

•   Source: SciCrunch Registry

http://dna.cs.byu.edu/gnumap/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. A probabilistic algorithm that addresses the computational problems associated with aligning bisulfite sequencing data to a reference genome.

Proper citation: GNUMAP-BS (RRID:SCR_005995) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.14/bioc/html/h5vc.html

Software package that contains functions to interact with tally data from Next-Generation Sequencing (NGS) experiments that is stored in HDF5 files.

Proper citation: h5vc (RRID:SCR_006039) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/cob87icW6z/cafe/wiki/Home

R software package for the detection of gross chromosomal abnormalities from gene expression microarray data.

Proper citation: CAFE (RRID:SCR_005983) Copy   

•   Source: SciCrunch Registry

http://epigenomegateway.wustl.edu/

Software tool for visualizing and interacting with whole-genome datasets. Browser hosts Human Epigenome Atlas data produced by Roadmap Epigenomics project, but its use of advanced, multi-resolution data formats and its user-friendly interface make it possible for investigators to upload and visualize their own data as custom tracks. Developed and maintained by Epigenome Informatics Group at Washington University in St. Louis.

Proper citation: WashU Epigenome Browser (RRID:SCR_006208) Copy   

•   Source: SciCrunch Registry

http://isaac.bioapps.biozentrum.uni-wuerzburg.de/isaac/modules/genome/species.xhtml

Web based tool to enable the analysis of sets of genes, transcripts and proteins under different biological viewpoints and to interactively modify these sets at any point of the analysis. Detailed history and snapshot information allows tracing each action. One can switch back to previous states and perform new analyses. Sets can be viewed in the context of genomes, protein functions, protein interactions, pathways, regulation, diseases and drugs. Additionally, users can switch between species with an automatic, orthology based translation of existing gene sets. Sets as well as results of analyses can be exchanged between members of groups.

Proper citation: InterSpecies Analysing Application using Containers (RRID:SCR_006243) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/fcros/

A fold change ranks ordering statistics based software for detecting differentially expressed genes.

Proper citation: FCROS (RRID:SCR_006195) 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

http://galaxyproject.org/

Open, web-based platform providing bioinformatics tools and services for data intensive genomic research. Platform may be used as a service or installed locally to perform, reproduce, and share complete analyses. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Community has created Galaxy instances in many different forms and for many different applications including Galaxy servers, cloud services that support Galaxy instances, and virtual machines and containers that can be easily deployed for your own server.The Galaxy team is a part of BX at Penn State, and the Biology and Mathematics and Computer Science departments at Emory University.Training Infrastructure as a Service (TIaaS) is a service offered by some UseGalaxy servers to specifically support training use cases.

Proper citation: Galaxy (RRID:SCR_006281) Copy   

•   Source: SciCrunch Registry

http://gensc.org/

An open-membership International community to promote mechanisms that standardize the description of genomes and the exchange and integration of genomic data. Community-driven standards have the best chance of success if developed within the auspices of international working groups. Participants in the GSC include biologists, computer scientists, those building genomic databases and conducting large-scale comparative genomic analyses, and those with experience of building community-based standards. The mission of the GSC is to work with the wider community towards: * the implementation of new genomic standards * methods of capturing and exchanging metadata * harmonization of metadata collection and analysis efforts across the wider genomics community

Proper citation: Genomic Standards Consortium (RRID:SCR_006273) Copy   

•   Source: SciCrunch Registry

http://www.megasoftware.net/mega-md/mega-md.php

Software to forecast the deleteriousness of non-synonymous single nucleotide variants (nsSNVs) using multiple methods and explore them in the context of the variability permitted in the long-term evolution of the affected positions. A web version (MEGA-MDW) is also available.

Proper citation: MEGA-MD (RRID:SCR_006403) Copy   

•   Source: SciCrunch Registry

http://www.uni-koeln.de/med-fak/cgars/

Software package to dissect random from non-random patterns in copy number data and thereby to assess significantly enriched somatic copy number aberrations (SCNA) across a set of tumor specimens or cell lines.

Proper citation: CGARS (RRID:SCR_006404) Copy   

•   Source: SciCrunch Registry

http://www2.warwick.ac.uk/fac/sci/systemsbiology/staff/ott/tools_and_software/wigwams

A computational tool for analyzing multiple gene expression time series data sets for the same organism. The goal is to determine if there is evidence for gene regulatory mechanisms that are shared by multiple different expression responses.

Proper citation: Wigwams (RRID:SCR_006400) Copy   

•   Source: SciCrunch Registry

http://www.unc.edu/~yunmli/betaseq/

Software to control Type-I error inflation in partially sequenced data for rare variant association testing. It is typically used to combine sequence and genotype data for the two stage design, in which individuals sequenced in stage one for variant detection are solely or predominantly cases then in stage two the discovered variants are genotyped in the remaining individuals. BETASEQ can work with any existing rare variant association methods that use genotypes or imputed genotypes as input.

Proper citation: BETASEQ (RRID:SCR_006401) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/IRanges/

Software tool for computing and annotating genomic ranges.Provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent Vector API as much as possible.

Proper citation: IRanges (RRID:SCR_006420) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/vicuna

A de novo assembly program targeting populations with high mutation rates.

Proper citation: VICUNA (RRID:SCR_006302) Copy   

•   Source: SciCrunch Registry