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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.
Open source and enterprise ready professional software for R statistical computing environment. Integrated development environment for R. Includes console, syntax highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. Available in open source and commercial editions and runs on desktop Windows, Mac, and Linux or in browser connected to RStudio Server or RStudio Server Pro (Debian/Ubuntu, RedHat/CentOS, and SUSE Linux).
Proper citation: RStudio (RRID:SCR_000432) Copy
http://drfast.sourceforge.net/
A software which maps di-base reads (SOLiD color space reads) to reference genome assemblies in a fast and memory-efficient manner.
Proper citation: drFAST (RRID:SCR_000586) Copy
http://genome.crg.es/software/gfftools/GFF2PS.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for visualizing annotations of genomic sequences. The program has features such as the ability to create comprehensive plots, customizable parameters, and flexibility in file format.
Proper citation: Genome BioInformatics Research Lab - gff2ps (RRID:SCR_000462) Copy
http://bioconductor.org/packages/release/bioc/html/Rdisop.html
Software for identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists.
Proper citation: Rdisop (RRID:SCR_000453) Copy
http://www.broadinstitute.org/cancer/cga/contest
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. A software tool (and method) for estimating the amount of cross-sample contamination in next generation sequencing data.
Proper citation: ContEst (RRID:SCR_000595) Copy
http://bioconductor.org/packages/release/bioc/html/flipflop.html
Software that discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data.
Proper citation: FlipFlop (RRID:SCR_000625) Copy
Discontinued
https://github.com/PacificBiosciences/blasr
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. C++ long-read aligner for PacBio reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: BLASR (RRID:SCR_000764) Copy
http://sourceforge.net/projects/gmcloser/
Software that fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased by successive treatments with different contig sets.
Proper citation: GMcloser (RRID:SCR_000646) Copy
https://github.com/shinout/clipcrop
Software tool for detecting structural variations with single-base resolution using soft-clipping information from SAM files.
Proper citation: clipcrop (RRID:SCR_000678) Copy
http://sourceforge.net/projects/triagetools/
A collection of tools for partitioning raw data (fastq reads) from high-throughput sequencing projects. The tools are designed for basic data management as well for prioritizing analysis of certain subsets.
Proper citation: TriageTools (RRID:SCR_000675) Copy
http://sourceforge.net/projects/operasf/
A sequence assembly software program that uses information from paired-end reads to optimally order and orient contigs assembled from shotgun-sequencing reads.
Proper citation: Opera (RRID:SCR_000665) Copy
http://pfind.ict.ac.cn/se/plink/
Software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: pFind Studio: pLink (RRID:SCR_000084) Copy
https://code.google.com/p/guardd/
MATLAB software designed to organize, automate, and enhance the analytical procedures which operate on CPMG RD NMR data.
Proper citation: GUARDD (RRID:SCR_000040) Copy
https://github.com/SciLifeLab/facs
Software for classification of Sequences using Bloom filters that can accurately and rapidly align sequences to a reference sequence.
Proper citation: FACS (RRID:SCR_000055) Copy
http://www.bioconductor.org/packages/release/bioc/html/GEOquery.html
Software that establishes a bridge between GEO and BioConductor.
Proper citation: GEOquery (RRID:SCR_000146) Copy
http://sourceforge.net/projects/gemsim/
A software package for generating realistic simulated next-generation genome sequencing reads with quality score values. The software is written in Python with a command-line user interface.
Proper citation: GemSIM (RRID:SCR_000167) Copy
http://www.bioconductor.org/packages/release/bioc/html/MIMOSA.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for modeling count data using Dirichlet-multinomial and beta-binomial mixtures with applications to single-cell assays.
Proper citation: MIMOSA (RRID:SCR_000184) Copy
http://acgt.cs.tau.ac.il/modent/
A computational tool that reconstructs gene regulatory networks from high throughput experimental data.
Proper citation: MODENT - A Tool For Reconstructing Gene Regulatory Networks (RRID:SCR_000220) Copy
https://github.com/vahuynh/dynGENIE3
An algorithm for the inference of gene regulatory networks from expression data.
Proper citation: GENIE3 (RRID:SCR_000217) Copy
http://www.uniklinikum-saarland.de/einrichtungen/fachrichtungen/humangenetik/software/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software tool for predicting granzyme B and caspase cleavage sites.
Proper citation: GraBCas (RRID:SCR_000205) Copy
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