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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GATB Resource Report Resource Website 1+ mentions |
GATB (RRID:SCR_024024) | software toolkit, software resource | Software genome analysis toolbox with de-Bruijn graph. Library dedicated to genome assembly and analysis. | genome assembly, genome analysis, | is listed by: Debian | PMID:24990603 | Free, Available for download, Freely available | OMICS_04834 | https://sources.debian.org/src/gatb-core/, https://gatb.inria.fr/software/gatb-core/ | SCR_024024 | GATB-CORE, gatb-core, GATB-TOOLS, The Genome Analysis Toolbox with de-Bruijn graph | 2026-08-05 10:47:57 | 3 | ||||||
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bambamc Resource Report Resource Website |
bambamc (RRID:SCR_023970) | software toolkit, software resource | Software package contains lightweight C implementation of name collating BAM file input and BAM file output. | C implementation, name collating BAM file input, BAM file output, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/bambamc/ | SCR_023970 | 2026-08-05 10:47:56 | 0 | |||||||||
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bamkit Resource Report Resource Website |
bamkit (RRID:SCR_023969) | software toolkit, software resource | Software tools for common BAM file manipulations. | BAM file manipulations, BAM file, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/bamkit/ | SCR_023969 | 2026-08-05 10:47:56 | 0 | |||||||||
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Atropos Resource Report Resource Website 1+ mentions |
Atropos (RRID:SCR_023962) | software application, source code, software resource | Software tool for specific, sensitive, and speedy trimming of NGS reads. | speedy trimming of NGS reads, NGS reads, Next Generation Sequencing, | is listed by: Debian | PMID:28875074 | Free, Available for download, Freely available | OMICS_20869 | https://sources.debian.org/src/atropos/ | SCR_023962 | atropos | 2026-08-05 10:47:56 | 3 | ||||||
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FAST Analysis of Sequences Toolbox Resource Report Resource Website |
FAST Analysis of Sequences Toolbox (RRID:SCR_024074) | FAST | software toolkit, software resource | Software Fast Analysis of Sequences Toolbox (FAST) is a set of UNIX utilities (for example fasgrep, fascut, fashead and fastr) that extends the UNIX toolbox paradigm to bioinformatic sequence records.FAST workflows are designed for serial processing of flatfile biological sequence record databases per-sequence, rather than per-line, through UNIX pipelines. The default data exchange format is multifasta (specifically, a restriction of BioPerl FastA format). FASTQ format is supported. FAST is designed for learnability, interoperability, interface consistency, rapid prototyping, fine-tuned control, and reproducibility. FAST tools expose the power of Perl and BioPerl to users in an easy-to-learn command-line paradigm. | Analysis of sequences, UNIX utilities, UNIX toolbox paradigm to bioinformatic sequence records, serial processing, flatfile biological sequence record databases per-sequence, FASTQ format, learnability, interoperability, interface consistency, rapid prototyping, fine-tuned control, reproducibility | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libfast-perl/ | SCR_024074 | libfast-perl, Fast Analysis of Sequences Toolbox, FAST - FAST Analysis of Sequences Toolbox, fast | 2026-08-05 10:47:57 | 0 | |||||||
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Bio-PrimerDesigner Resource Report Resource Website |
Bio-PrimerDesigner (RRID:SCR_024082) | software toolkit, software resource | Software package provides low-level interface to the primer3 and epcr binary executables and supplies methods to return the results. Because primer3 and e-PCR are only available for Unix-like operating systems, Bio-PrimerDesigner offers the ability to accessing the primer3 binary via a remote server. Local installations of primer3 or e-PCR on Unix hosts are also supported. | interface to the primer3 and epcr binary executables, methods to return the results, accessing primer3 binary via remote server, Unix hosts supported, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-primerdesigner-perl/ | SCR_024082 | Bio-PrimerDesigner - Design PCR Primers using primer3 and epcr, libbio-primerdesigner-perl | 2026-08-05 10:47:58 | 0 | ||||||||
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rasmol Resource Report Resource Website 10+ mentions |
rasmol (RRID:SCR_024208) | software toolkit, software resource | Software package for molecular graphics visualisation.Used for visualisation of molecules. | biomolecular graphics, molecules visualisation, | is listed by: Debian | PMID:7482707 | Free, Available for download, Freely available, | OMICS_05076 | https://sources.debian.org/src/rasmol/ | SCR_024208 | RasMol | 2026-08-05 10:48:00 | 13 | ||||||
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Raster3D Resource Report Resource Website |
Raster3D (RRID:SCR_024220) | software toolkit, software resource | Software tools for generating high quality raster images of proteins or other molecules. Photorealistic molecular graphics. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. | generating high quality raster images, protein images, molecules images, images generation, molecular graphics, | is listed by: Debian | PMID:18488322 | Free, Available for download, Freely available, | OMICS_05054 | https://sources.debian.org/src/raster3d/ | SCR_024220 | raster3d | 2026-08-05 10:48:00 | 0 | ||||||
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Biobase Resource Report Resource Website 10+ mentions |
Biobase (RRID:SCR_024224) | software toolkit, software resource | Software R package provides functions that are needed by many other packages or which replace R functions. Base functions for Bioconductor. | Base functions for Bioconductor, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-biobase/ | SCR_024224 | 2026-08-05 10:48:01 | 28 | |||||||||
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fitbitscraper Resource Report Resource Website |
fitbitscraper (RRID:SCR_024273) | software toolkit, software resource | Software R package to scrape data from Fitbit to generate graphs. | generate graphs, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-fitbitscraper/ | SCR_024273 | 2026-08-05 10:48:01 | 0 | |||||||||
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fitdistrplus Resource Report Resource Website 1+ mentions |
fitdistrplus (RRID:SCR_024274) | software toolkit, software resource | Software R package extends fitdistr function to help the fit of parametric distribution to non-censored or censored data. | extend fitdistr function, parametric distribution fit, non-censored or censored data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-fitdistrplus/ | SCR_024274 | 2026-08-05 10:48:01 | 1 | |||||||||
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DT Resource Report Resource Website 1+ mentions |
DT (RRID:SCR_024270) | software toolkit, software resource | Software R package for data objects in R to render as HTML tables using JavaScript library DataTables. DataTables library has been included in this R package. | data objects in R, HTML tables, JavaScript library DataTables, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-dt/ | SCR_024270 | DT: A Wrapper of the JavaScript Library 'DataTables', r-cran-dt, DataTables | 2026-08-05 10:48:01 | 3 | ||||||||
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PiGx-RNAseq Resource Report Resource Website |
PiGx-RNAseq (RRID:SCR_024160) | software toolkit, software resource | Software reproducible genomics analysis pipelines with GNU Guix. Used for analysis of RNA sequencing, chromatin immunoprecipitation sequencing, bisulfite-treated DNA sequencing, and single-cell resolution RNA sequencing. All pipelines process raw experimental data and generate reports containing publication-ready plots and figures, with interactive report elements and standard observables. | reproducible genomics analysis pipelines, GNU Guix, RNA sequencing analysis, chromatin immunoprecipitation sequencing analysis, bisulfite-treated DNA sequencing analysis, single cell resolution RNA sequencing analysis, | is listed by: Debian | PMID:30277498 | Free, Available for download, Freely available, | OMICS_33677 | https://sources.debian.org/src/pigx-rnaseq/ | SCR_024160 | pigx-rnaseq | 2026-08-05 10:47:59 | 0 | ||||||
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rbgl Resource Report Resource Website |
rbgl (RRID:SCR_024251) | software toolkit, software resource | Software R package as interface to the graph algorithms contained in the BOOST library. | interface to the graph algorithm, BOOST library, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-rbgl/ | SCR_024251 | 2026-08-05 10:48:01 | 0 | |||||||||
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pcaMethods Resource Report Resource Website 10+ mentions |
pcaMethods (RRID:SCR_024252) | software toolkit, software resource | Software R package providing PCA methods for incomplete data. Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and conventional SVD PCA. Cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. | PCA methods for incomplete data, missing value estimation, | is listed by: Debian | PMID:17344241 | Free, Available for download, Freely available, | OMICS_14344 | https://sources.debian.org/src/r-bioc-pcamethods/ | SCR_024252 | pcamethods | 2026-08-05 10:48:00 | 11 | ||||||
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rcpi Resource Report Resource Website |
rcpi (RRID:SCR_024253) | software toolkit, software resource | Software R package as molecular informatics toolkit with integration of bioinformatics and chemoinformatics tools for drug discovery. | drug discovery, bioinformatics and chemoinformatics integration, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-rcpi/ | SCR_024253 | 2026-08-05 10:48:00 | 0 | |||||||||
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rgsepd Resource Report Resource Website |
rgsepd (RRID:SCR_024256) | software toolkit, software resource | Software R package to help disambiguate transcriptome samples by automating differential expression, then gene set enrichment, and finally N-dimensional projection to quantify in which ways each sample is like either treatment group. | disambiguate transcriptome samples, automating differential expression, gene set enrichment, N-dimensional projection, treatment group, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-rgsepd/ | SCR_024256 | 2026-08-05 10:48:01 | 0 | |||||||||
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makecdfenv Resource Report Resource Website 1+ mentions |
makecdfenv (RRID:SCR_024248) | software toolkit, software resource | Software R package has two functions. One reads Affymetrix chip description file and creates hash table environment containing location/probe set membership mapping. The other creates package that automatically loads that environment. | read Affymetrix chip description file, create hash table environment, location, probe, set membership mapping, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-makecdfenv/ | SCR_024248 | 2026-08-05 10:48:01 | 1 | |||||||||
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beeswarm Resource Report Resource Website |
beeswarm (RRID:SCR_024262) | software toolkit, software resource | Software R package implementing bee swarm plots. Bee swarm plot is one-dimensional scatter plot like "stripchart", but with closely packed, non overlapping points. | bee swarm plots, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-beeswarm/ | SCR_024262 | an Alternative to Stripchart, r-cran-beeswarm, The Bee Swarm Plot, beeswarm: The Bee Swarm Plot | 2026-08-05 10:48:01 | 0 | ||||||||
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adephylo Resource Report Resource Website 1+ mentions |
adephylo (RRID:SCR_024267) | software toolkit, software resource | Software R package provides multivariate tools to analyze comparative data. Analysis of comparative evolutionary data. Used for investigating phylogenetic signal in biological traits. | analyze comparative data, investigating phylogenetic signal, biological traits, investigating phylogenetic signal in biological traits, comparative evolutionary data analysis, | is listed by: Debian | PMID:20525823 | Free, Available for download, Freely available, | OMICS_08682 | https://sources.debian.org/src/r-cran-adephylo/ | SCR_024267 | 2026-08-05 10:48:00 | 3 |
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