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http://www.genome.gov/Glossary/

Glossary of Genetic Terms to help everyone understand the terms and concepts used in genetic research. In addition to definitions, specialists in the field of genetics share their descriptions of terms, and many terms include images, animation and links to related terms.

Proper citation: Talking Glossary of Genetic Terms (RRID:SCR_003215) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/mouseportal/

Database of mouse research resources at Sanger: BACs, targeting vectors, targeted ES cells, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen. The Wellcome Trust Sanger Institute generates, characterizes, and uses a variety of reagents for mouse genetics research. It also aims to facilitate the distribution of these resources to the external scientific community. Here, you will find unified access to the different resources available from the Institute or its collaborators. The resources include: 129S7 and C57BL6/J bacterial artificial chromosomes (BACs), MICER gene targeting vectors, knock-out first conditional-ready gene targeting vectors, embryonic stem (ES) cells with gene targeted mutations or with retroviral gene trap insertions, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen.

Proper citation: Sanger Mouse Resources Portal (RRID:SCR_006239) Copy   

•   Source: SciCrunch Registry

http://chgr.mc.vanderbilt.edu/page/gist

Software package to test if a marker can account in part for the linkage signal in its region. There are two versions of the software: Windows and Linux/Unix.

Proper citation: Genotype-IBD Sharing Test (RRID:SCR_006257) Copy   

•   Source: SciCrunch Registry

https://github.com/caraweisman/abSENSE

Software to interpret undetected homolog.Method that calculates probability that homolog of given gene would fail to be detected by homology search in given species, even if homolog were present and evolving normally.

Proper citation: abSENSE (RRID:SCR_023223) Copy   

•   Source: SciCrunch Registry

https://github.com/genome/bam-readcount

Software tool that runs on BAM or CRAM file and generates low level information about sequencing data at specific nucleotide positions. Its outputs include observed bases, readcounts, summarized mapping and base qualities, strandedness information, mismatch counts, and position within the reads.

Proper citation: bam readcount (RRID:SCR_023653) Copy   

•   Source: SciCrunch Registry

https://github.com/churchmanlab/genewalk

Software for individual genes functions determination that are relevant in particular biological context and experimental condition. Quantifies similarity between vector representations of gene and annotated GO terms through representation learning with random walks on condition specific gene regulatory network. Similarity significance is determined through comparison with node similarities from randomized networks.

Proper citation: GeneWalk (RRID:SCR_023787) Copy   

•   Source: SciCrunch Registry

https://github.com/tobiasrausch/alfred

Web application as interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencingas.

Proper citation: Alfred (RRID:SCR_023354) Copy   

•   Source: SciCrunch Registry

http://crispor.tefor.net

Web application that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system. This sgRNA design tool assists with guide selection in a variety of genomes and pre-calculated results for all human coding exons as a UCSC Genome Browser track.

Proper citation: CRISPOR (RRID:SCR_015935) Copy   

•   Source: SciCrunch Registry

https://github.com/hahnlab/CAFExp

Software tool for computational analysis of gene family evolution. Used for statistical analysis of evolution gene family sizes. Models evolution of gene family sizes over phylogeny.

Proper citation: Computational Analysis of gene Family Evolution (RRID:SCR_018924) Copy   

•   Source: SciCrunch Registry

https://github.com/broadinstitute/Drop-seq

Software Java tools for analyzing Drop-seq data. Used to analyze gene expression from thousands of individual cells simultaneously. Analyzes mRNA transcripts while remembering origin cell transcript.

Proper citation: Drop-seq tools (RRID:SCR_018142) Copy   

•   Source: SciCrunch Registry

https://github.com/sreeramkannan/Shannon

Software tool for de novo transcriptome assembly from RNA-Seq data.

Proper citation: Shannon (RRID:SCR_017037) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/SNPRelate/

Software R package as parallel computing toolset for relatedness and principal component analysis of SNP data.

Proper citation: SNPRelate (RRID:SCR_022719) Copy   

•   Source: SciCrunch Registry

https://github.com/xfengnefx/hifiasm-meta

Software tool as metagenome assembler that exploits high accuracy of recent data. De novo metagenome assembler, based on haplotype resolved de novo assembler for PacBio Hifi reads. Workflow consists of optional read selection, sequencing error correction, read overlapping, string graph construction and graph cleaning.

Proper citation: hifiasm-meta (RRID:SCR_022771) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=ComplexUpset

Software R package for visualization of intersecting sets. Used for quantitative analysis of sets, their intersections, and aggregates of intersections. Visualizes set intersections in matrix layout and introduces aggregates based on groupings and queries.

Proper citation: ComplexUpset (RRID:SCR_022752) Copy   

•   Source: SciCrunch Registry

https://reich.hms.harvard.edu/software

Software application that finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. It can be downloaded for either UNIX or Linux.

Proper citation: Ancestrymap (RRID:SCR_004353) Copy   

•   Source: SciCrunch Registry

http://compbio.mit.edu/ChromHMM/

Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations.

Proper citation: ChromHMM (RRID:SCR_018141) Copy   

•   Source: SciCrunch Registry

http://tripod.nih.gov/npc/

The NCGC Pharmaceutical Collection (NPC) is a comprehensive, publically-accessible collection of approved and investigational drugs for high-throughput screening that provides a valuable resource for both validating new models of disease and better understanding the molecular basis of disease pathology and intervention. The NPC has already generated several useful probes for studying a diverse cross section of biology, including novel targets and pathways. NCGC provides access to its set of approved drugs and bioactives through the Therapeutics for Rare and Neglected Diseases (TRND) program and as part of the compound collection for the Tox21 initiative, a collaborative effort for toxicity screening among several government agencies including the US Environmental Protection Agency (EPA), the National Toxicology Program (NTP), the US Food and Drugs Administration (FDA), and the NCGC. Of the nearly 2750 small molecular entities (MEs) that have been approved for clinical use by US (FDA), EU (EMA), Japanese (NHI), and Canadian (HC) authorities and that are amenable to HTS screening, we currently possess 2,400 as part of our screening collection. The NPC resource currently consists of (i) the physical collection suitable for high throughput screening (HTS) and (ii) the informatics browser and database. Putting together the physical collection has been surprisingly challenging in terms of the time and effort required in the informatics, compound management and synthetic chemistry related activities required for this endeavor. We provide access to the NPC screening library through collaboration. Please contact our Scientific Director Dr. Chris Austin for additional information. The other half of the NPC resource is the NPC browser. This is a self-contained software that is actively developed and maintained by the informatics group to provide electronic access to the NPC content. The latest version of the NPC browser for various platforms can be downloaded.

Proper citation: NCGC Pharmaceutical Collection (RRID:SCR_006909) 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://www.pathwaycommons.org/pc

Database of publicly available pathways from multiple organisms and multiple sources represented in a common language. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes. Pathways were downloaded directly from source databases. Each source pathway database has been created differently, some by manual extraction of pathway information from the literature and some by computational prediction. Pathway Commons provides a filtering mechanism to allow the user to view only chosen subsets of information, such as only the manually curated subset. The quality of Pathway Commons pathways is dependent on the quality of the pathways from source databases. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. It currently contains data from nine databases with over 1,668 pathways, 442,182 interactions,414 organisms and will be continually expanded and updated. (April 2013)

Proper citation: Pathway Commons (RRID:SCR_002103) Copy   

•   Source: SciCrunch Registry

http://htslib.org/

Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.

Proper citation: SAMTOOLS (RRID:SCR_002105) Copy   

•   Source: SciCrunch Registry