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https://cran.r-project.org/web/packages/DoseFinding/index.html

Software R package provides functions for design and analysis of dose finding experiments. Used for multiple contrast tests, fitting non-linear dose-response models, calculating optimal designs and implementation of MCPMod methodology.

Proper citation: DoseFinding (RRID:SCR_024268) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/distory/index.html

Software R package for geodesic distance between phylogenetic trees and associated functions.

Proper citation: distory (RRID:SCR_024269) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=Rwave

Software R package provides environment for Time-Frequency analysis of 1-D signals.

Proper citation: rwave (RRID:SCR_024302) Copy   

•   Source: SciCrunch Registry

https://github.com/vals/umis

Software tools for estimating expression in RNA-Seq data which performs sequencing of end tags of transcript, and incorporate molecular tags to correct for amplification bias.

Proper citation: umis (RRID:SCR_024381) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/alakazam/index.html

Software R package for high-throughput adaptive immune receptor repertoire sequencing analysis. In particular, immunoglobulin sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage.

Proper citation: alakazam (RRID:SCR_024261) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/ade4/index.html

Software R package for multivariate data analysis. Used for analysis of one-table, two-table, three-table and K-table.

Proper citation: ade4 (RRID:SCR_024259) Copy   

•   Source: SciCrunch Registry

https://github.com/ncbi/sra-tools/

Software collection of tools and libraries for using data in the INSDC Sequence Read Archives.Used for long term storage of the next-generation sequence traces.

Proper citation: sra-toolkit (RRID:SCR_024350) Copy   

•   Source: SciCrunch Registry

http://metabarcoding.org/sumaclust

Software tool aims to cluster sequences in a way that is fast and exact at the same time.

Proper citation: sumaclust (RRID:SCR_024352) Copy   

•   Source: SciCrunch Registry

http://swissknife.sourceforge.net

Software object oriented Perl library to handle Swiss-Prot entries

Proper citation: libswiss-perl (RRID:SCR_024356) Copy   

•   Source: SciCrunch Registry

https://graphics.stanford.edu/software/volpack/

Portable software library for volume rendering.

Proper citation: VolPack (RRID:SCR_024367) Copy   

•   Source: SciCrunch Registry

http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/

A system of databases which stores information on the influence of mutations in regulatory gene regions . This tool helps recognize protein binding sites that are being altered by mutation. It has four cross-linked sub databases that focus on specific aspects including: (1) the effect of single nucleotide mutations in regulatory gene regions and their interaction with nuclear proteins; (2) references to original publications on the subject; (3) the experimental details of these publications; and (4) the protocols of these experiments. This resource is aimed at providing information to further research on the influence of specific sequence alterations on disease susceptibility, drug resistance and healthcare.

Proper citation: rSNP Guide (RRID:SCR_000087) Copy   

•   Source: SciCrunch Registry

http://www.proglycprot.org/

Manually curated, comprehensive repository of experimentally characterized bacterial glycoproteins and archaeal glycoproteins, generated from an exhaustive literature search. This is the focused effort to provide concise relevant information derived from rapidly expanding literature on prokaryotic glycoproteins, their glycosylating enzyme(s), glycosylation linked genes, and genomic context thereof, in a cross-referenced manner. The database is arranged into two sections namely, ProCGP and ProUGP. ProCGP is the main section containing characterized prokaryotic glycoproteins, defined as entries with at least one experimentally known glycosylated residue (glycosite). Whereas, ProUGP is the supplementary section, presenting uncharacterized prokaryotic glycoproteins, defined as entries with experimentally identified glycosylation but unidentified glycosites. The ProGlycProt has been developed with to aid and advance the emerging scientific interests in understanding the mechanisms, implications, and novelties of protein glycosylation in prokaryotes that include many pathogenic as well as economically important bacterial species. The website supports a dedicated structure gallery of homology models and crystal structures of characterized glycoproteins in addition to two new tools developed in view of emerging information about prokaryotic sequons (conserved sequences of amino acids around glycosites) that are never or rarely seen in eukaryotic glycoproteins. ProGlycProt provides an extensive compilation of experimentally identified glycosites (334) and glycoproteins (340) of prokaryotes that could serve as an information resource for research and technology applications in glycobiology. A general data update policy is once in three months. Existing entries are updated in real-time.

Proper citation: ProGlycProt (RRID:SCR_000622) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/dbSTS/

THIS RESOURCE IS NO LONGER IN SERVICE, as of October 1, 2013; however, the site is still accessible. NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites. STS sequences are incorporated into the STS Division of GenBank. The dbSTS database offers a route for submission of STS sequences to GenBank. It is designed especially for the submission of large batches of STS sequences.

Proper citation: dbSTS (RRID:SCR_000400) Copy   

•   Source: SciCrunch Registry

http://interolog.gersteinlab.org/

Interolog/Regulog quantitatively assess the degree to which interologs can be reliably transferred between species as a function of the sequence similarity of the corresponding interacting proteins.

Proper citation: Interolog/Regulog Database (RRID:SCR_000755) Copy   

•   Source: SciCrunch Registry

http://www.homozygositymapper.org/

A web-based approach of homozygosity mapping that can handle tens of thousands markers. User can upload their own SNP genotype files to the database. Intuitive graphic interface is provided to view the homozygous stretches, with the ability of zooming into single chromosomes or user-defined chromosome regions. The underlying genotypes in all samples are displayed. The software is also integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. (entry from Genetic Analysis Software)

Proper citation: HOMOZYGOSITYMAPPER (RRID:SCR_001714) Copy   

•   Source: SciCrunch Registry

http://www.bioguo.org/AnimalTFDB/

A comprehensive transcription factor (TF) database in which they identified and classified all the genome-wide TFs in 50 sequenced animal genomes (Ensembl release version 60). In addition to TFs, it also collects transcription co-factors and chromatin remodeling factors of those genomes, which play regulatory roles in transcription. Here they defined the TFs as proteins containing a sequence-specific DNA-binding domain (DBD) and regulating target gene expression. Currently, the AnimalTFDB classifies all the animal TFs into 72 families according to their conserved DBDs. Gene lists of transcription factors, transcription co-factors and chromatin remodeling factors of each species are available for downloading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: AnimalTFDB (RRID:SCR_001624) Copy   

•   Source: SciCrunch Registry

https://www.hgmd.cf.ac.uk/ac/introduction.php?lang=english

Curated database of known (published) gene lesions responsible for human inherited disease.

Proper citation: Human Gene Mutation Database (RRID:SCR_001621) Copy   

•   Source: SciCrunch Registry

http://labs.europepmc.org/evf

A web application to assist in the identification of articles and research related to literature search terms. The search covers full text articles in the Europe PMC repository. Relevant papers are suggested to users based on the scientific term searched and the selection of questions, generated by the application, relevant to term searched.

Proper citation: EvidenceFinder (RRID:SCR_013764) Copy   

•   Source: SciCrunch Registry

http://www.mricro.com

Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.

Proper citation: MRIcron (RRID:SCR_002403) Copy   

•   Source: SciCrunch Registry

https://github.com/qmarcou/IGoR/

C++ software designed to infer V(D)J recombination related processes from sequencing data.

Proper citation: IGoR (RRID:SCR_024053) Copy   

•   Source: SciCrunch Registry