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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://cran.r-project.org/package=psychotree
Software R package for recursive partitioning based on psychometric models, employing general MOB algorithm to obtain Bradley-Terry trees, Rasch trees, rating scale and partial credit trees, and MPT trees, trees for 1PL, 2PL, 3PL and 4PL models and generalized partial credit models.
Proper citation: psychotree (RRID:SCR_024288) Copy
http://saint-apms.sourceforge.net/Main.html
Software package for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments.
Proper citation: saint (RRID:SCR_024324) Copy
https://cran.r-project.org/web/packages/dynamicTreeCut/index.html
Software R package contains methods for detection of clusters in hierarchical clustering dendrograms.
Proper citation: dynamicTreeCut (RRID:SCR_024280) Copy
https://github.com/artic-network/readucks
Software package as Nanopore read de-multiplexer.
Proper citation: readucks (RRID:SCR_024315) Copy
https://cran.r-project.org/package=stringi
Software R package as collection of character string/text/natural language processing tools for pattern searching, random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date time formatting and parsing.
Proper citation: stringi (RRID:SCR_024319) Copy
Software tool for automated drawing, visualization and annotation of secondary structure of RNA, designed as companion software for web servers and databases.Allows manual modification and structural annotation of resulting drawing using either interactive point and click approach, within web server or through command-line arguments.
Proper citation: VARNA (RRID:SCR_024373) Copy
https://github.com/vgteam/vg#vg
Software toolkit to improve read mapping by representing genetic variation in reference.Provides succinct encoding of sequences of many genomes.
Proper citation: variation graph (RRID:SCR_024369) Copy
https://sourceforge.net/projects/trinculo/
Software toolkit for carrying out genetic association for multi-catagory phenotypes. Implements multinomial and ordinal association incorporating covariates, conditional analysis, empirical and non-emperical priors and fine-mapping.
Proper citation: Trinculo (RRID:SCR_024384) Copy
https://cran.r-project.org/package=Rwave
Software R package provides environment for Time-Frequency analysis of 1-D signals.
Proper citation: rwave (RRID:SCR_024302) Copy
Software tools for estimating expression in RNA-Seq data which performs sequencing of end tags of transcript, and incorporate molecular tags to correct for amplification bias.
Proper citation: umis (RRID:SCR_024381) Copy
https://github.com/ncbi/sra-tools/
Software collection of tools and libraries for using data in the INSDC Sequence Read Archives.Used for long term storage of the next-generation sequence traces.
Proper citation: sra-toolkit (RRID:SCR_024350) Copy
Software R-package for running gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. The Piano package contains functions for combining the results of multiple runs of gene set analyses.
Proper citation: Piano (RRID:SCR_003200) Copy
http://www.broadinstitute.org/cancer/software/genepattern
A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.
Proper citation: GenePattern (RRID:SCR_003201) Copy
Software package for nucleic acid folding and hybridization prediction. It has capabilities to predict folding for single-stranded RNA or DNA through a combination of free energy minimization, partition function calculations and stochastic sampling. The program runs on Unix and Linux platforms as well as Mac OS X and Windows.
Proper citation: UNAFold (RRID:SCR_001360) Copy
http://www.geenivaramu.ee/en/tools/gwama
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for meta analysis of whole genome association data.
Proper citation: GWAMA (RRID:SCR_006624) Copy
http://bioconductor.org/packages/release/bioc/html/DESeq.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Software for differential gene expression analysis based on the negative binomial distribution. It estimates variance-mean dependence in count data from high-throughput sequencing assays and tests for differential expression.
Proper citation: DESeq (RRID:SCR_000154) Copy
https://sourceforge.net/projects/popbam/
A tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome.
Proper citation: POPBAM (RRID:SCR_000464) Copy
http://code.google.com/p/gasv/
Software tool for identifying structural variants (SVs) from paired-end sequencing data.GASV distribution includes three components that are typically run in succession: the BAM file of unique paired-read mappings is processed; structural variants are identified by clustering discordant fragments; and a probabilistic algorithm improves the specificity of GASV predictions.
Proper citation: GASV (RRID:SCR_000061) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data, but also supporting analysis of other types of data. QIMME analyzes and transforms raw sequencing data generated on Illumina or other platforms to publication quality graphics and statistics.
Proper citation: QIIME (RRID:SCR_008249) Copy
https://github.com/lpantano/seqbuster
Software tool for processing and analysis of small RNAs datasets.Reveals ubiquitous miRNA modifications in human embryonic cells.
Proper citation: SeqBuster (RRID:SCR_009616) Copy
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