Tools   Select Another Resource Report Type

https://github.com/yongchao/flowPeaks

Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.

Proper citation: flowPeaks (RRID:SCR_000407) Copy   

•   Source: SciCrunch Registry

http://proteinprophet.sourceforge.net/

Software that automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST.

Proper citation: ProteinProphet (RRID:SCR_000286) Copy   

•   Source: SciCrunch Registry

https://github.com/feizhe/PGS

Software tool for association study of high-dimensional microRNA expression data with repeated measures. The penalized regression model incorporates a grid search method for analyzing associations of high-dimensional microRNA expression data with repeated measures.

Proper citation: PGS (RRID:SCR_000475) Copy   

•   Source: SciCrunch Registry

http://mfuzz.sysbiolab.eu/

Software package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Mfuzz (RRID:SCR_000523) Copy   

•   Source: SciCrunch Registry

http://gmt.genome.wustl.edu/pindel/0.2.4/

Software to detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Pindel (RRID:SCR_000560) Copy   

•   Source: SciCrunch Registry

http://paleogenomics.irmacs.sfu.ca/FPSAC/

Sogftware for fast Phylogenetic Scaffolding of Ancient Contigs.

Proper citation: FPSAC (RRID:SCR_000555) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry