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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://github.com/GATB/gatb-core
Software genome analysis toolbox with de-Bruijn graph. Library dedicated to genome assembly and analysis.
Proper citation: GATB (RRID:SCR_024024) Copy
https://github.com/gt1/bambamc
Software package contains lightweight C implementation of name collating BAM file input and BAM file output.
Proper citation: bambamc (RRID:SCR_023970) Copy
https://github.com/hall-lab/bamkit
Software tools for common BAM file manipulations.
Proper citation: bamkit (RRID:SCR_023969) Copy
https://github.com/jdidion/atropos
Software tool for specific, sensitive, and speedy trimming of NGS reads.
Proper citation: Atropos (RRID:SCR_023962) Copy
https://metacpan.org/dist/FAST
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.
Proper citation: FAST Analysis of Sequences Toolbox (RRID:SCR_024074) Copy
https://metacpan.org/dist/Bio-PrimerDesigner
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.
Proper citation: Bio-PrimerDesigner (RRID:SCR_024082) Copy
Software package for molecular graphics visualisation.Used for visualisation of molecules.
Proper citation: rasmol (RRID:SCR_024208) Copy
http://www.bmsc.washington.edu/raster3d/raster3d.html
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.
Proper citation: Raster3D (RRID:SCR_024220) Copy
https://bioconductor.org/packages/release/bioc/html/Biobase.html
Software R package provides functions that are needed by many other packages or which replace R functions. Base functions for Bioconductor.
Proper citation: Biobase (RRID:SCR_024224) Copy
https://cran.r-project.org/web/packages/fitbitScraper/index.html
Software R package to scrape data from Fitbit to generate graphs.
Proper citation: fitbitscraper (RRID:SCR_024273) Copy
https://cran.r-project.org/web/packages/fitdistrplus/index.html
Software R package extends fitdistr function to help the fit of parametric distribution to non-censored or censored data.
Proper citation: fitdistrplus (RRID:SCR_024274) Copy
https://cran.r-project.org/web/packages/DT/index.html
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.
Proper citation: DT (RRID:SCR_024270) Copy
https://github.com/BIMSBbioinfo/pigx_rnaseq
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.
Proper citation: PiGx-RNAseq (RRID:SCR_024160) Copy
https://bioconductor.org/packages/RBGL/
Software R package as interface to the graph algorithms contained in the BOOST library.
Proper citation: rbgl (RRID:SCR_024251) Copy
https://bioconductor.org/packages/release/bioc/html/pcaMethods.html
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.
Proper citation: pcaMethods (RRID:SCR_024252) Copy
https://bioconductor.org/packages/Rcpi/
Software R package as molecular informatics toolkit with integration of bioinformatics and chemoinformatics tools for drug discovery.
Proper citation: rcpi (RRID:SCR_024253) Copy
https://bioconductor.org/packages/release/bioc/html/rgsepd.html
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.
Proper citation: rgsepd (RRID:SCR_024256) Copy
https://bioconductor.org/packages/makecdfenv/
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.
Proper citation: makecdfenv (RRID:SCR_024248) Copy
https://cran.r-project.org/web/packages/beeswarm/index.html
Software R package implementing bee swarm plots. Bee swarm plot is one-dimensional scatter plot like "stripchart", but with closely packed, non overlapping points.
Proper citation: beeswarm (RRID:SCR_024262) Copy
https://cran.r-project.org/web/packages/adephylo/index.html
Software R package provides multivariate tools to analyze comparative data. Analysis of comparative evolutionary data. Used for investigating phylogenetic signal in biological traits.
Proper citation: adephylo (RRID:SCR_024267) Copy
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