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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.
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
https://github.com/cc2qe/speedseq
Software for a lightweight, flexible, and open source pipeline that identifies genomic variation (single nucleotide variants (SNVs), indels, and structural variants (SVs)).
Proper citation: SpeedSeq (RRID:SCR_000469) Copy
https://github.com/yhwu/matchclips/
Software program that detects the precise break points of Copy number variations (CNVs) through a fuzzy string matching algorithm using both CIGAR and POS information. In case the two break points of a CNV are in repeated regions and the break points are not unique, it reports the range where the break points can slide.
Proper citation: MATCHCLIP (RRID:SCR_000541) Copy
http://www.bioconductor.org/packages/release/bioc/html/TDARACNE.html
Software package to infer gene regulatory networks from time-series measurements. The algorithm is expected to be useful in reconstruction of small biological directed networks from time course data.
Proper citation: TDARACNE (RRID:SCR_000498) Copy
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
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
http://www.broadinstitute.org/genome_bio/siphy/
Software that implements rigorous statistical tests to detect bases under selection from a multiple alignment data. It takes full advantage of deeply sequenced phylogenies to estimate both unlikely substitution patterns as well as slowdowns or accelerations in mutation rates. It can be applied as an Hidden Markov Model (HMM), in sliding windows, or to specific regions.
Proper citation: SiPhy (RRID:SCR_000564) Copy
https://github.com/NetherlandsMetabolomicsCentre/TNO-DECO
Matlab code for preprocessing gas chromatography mass spectrometry data.
Proper citation: TNO-DECO (RRID:SCR_000440) Copy
http://lilab.stanford.edu/SNPiR/
Software for reliable Identification of Genomic Variants Using RNA-seq Data.
Proper citation: SNPiR (RRID:SCR_000557) Copy
http://paleogenomics.irmacs.sfu.ca/FPSAC/
Sogftware for fast Phylogenetic Scaffolding of Ancient Contigs.
Proper citation: FPSAC (RRID:SCR_000555) Copy
http://bbc.mdc-berlin.de/software
Multi-purpose SNV calling software enhanced by probabilistic integration of quality scores.
Proper citation: ACCUSA2 (RRID:SCR_000558) Copy
https://code.google.com/p/dysc/
Software for Greedy Clustering of 16S rRNA Reads which uses a dynamic seeding strategy.
Proper citation: DySC (RRID:SCR_000553) 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://bioinfo2.ugr.es/NGSmethPipe/
A software tool which generates high-quality methylation maps.
Proper citation: NGSmethPipe (RRID:SCR_000583) Copy
https://cran.r-project.org/src/contrib/Archive/sybil/
A Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). This is an implementation of COBRA toolbox in R language.
Proper citation: sybil - Efficient Constrained Based Modelling in R (RRID:SCR_000457) Copy
https://github.com/holtjma/msbwt
A software package for creating, merging, and querying multi-string BWTs.
Proper citation: msbwt (RRID:SCR_000458) 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
https://github.com/PacificBiosciences/stsPlots
Software to plot primary analysis quality control metrics to assess potential SMRTcell loading problems.
Proper citation: stsPlots (RRID:SCR_000449) 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
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