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

Software R package for modeling and monitoring of time series of counts, proportions and categorical data, as well as for modeling of continuous-time point processes of epidemic phenomena.

Proper citation: surveillance (RRID:SCR_024304) Copy   

•   Source: SciCrunch Registry

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

Softare R package as implementation of the t-SNE algorithm.

Proper citation: tsne (RRID:SCR_024305) Copy   

•   Source: SciCrunch Registry

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

Software R package provides interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling comprehensive phylogenetic tree for all named species.

Proper citation: rotl (RRID:SCR_024306) Copy   

•   Source: SciCrunch Registry

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

Software R package usability wrapper around snow for easier development of parallel R programs. This package offers e.g. extended error checks, and additional functions. All functions work in sequential mode if no cluster is present or wished. Package is also designed as connector to the cluster management tool sfCluster, but can also used without it.

Proper citation: snowfall (RRID:SCR_024309) Copy   

•   Source: SciCrunch Registry

http://saint-apms.sourceforge.net/Main.html

Software package for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments.

Proper citation: saint (RRID:SCR_024324) Copy   

•   Source: SciCrunch Registry

https://github.com/artic-network/readucks

Software package as Nanopore read de-multiplexer.

Proper citation: readucks (RRID:SCR_024315) Copy   

•   Source: SciCrunch Registry

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

Software R package as collection of character string/text/natural language processing tools for pattern searching, random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date time formatting and parsing.

Proper citation: stringi (RRID:SCR_024319) Copy   

•   Source: SciCrunch Registry

http://varna.lri.fr/

Software tool for automated drawing, visualization and annotation of secondary structure of RNA, designed as companion software for web servers and databases.Allows manual modification and structural annotation of resulting drawing using either interactive point and click approach, within web server or through command-line arguments.

Proper citation: VARNA (RRID:SCR_024373) Copy   

•   Source: SciCrunch Registry

https://github.com/vgteam/vg#vg

Software toolkit to improve read mapping by representing genetic variation in reference.Provides succinct encoding of sequences of many genomes.

Proper citation: variation graph (RRID:SCR_024369) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/trinculo/

Software toolkit for carrying out genetic association for multi-catagory phenotypes. Implements multinomial and ordinal association incorporating covariates, conditional analysis, empirical and non-emperical priors and fine-mapping.

Proper citation: Trinculo (RRID:SCR_024384) 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://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://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.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://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