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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.
http://www.scienceexchange.com/facilities/ksf-labs
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 3rd, 2022. KSF Labs is the virtual/real workshop(s).
Proper citation: KSF Labs (RRID:SCR_010987) Copy
Founded in 1995 with intention of making DNA sequencing and genotyping laboratory to provide DNA sequencing and genotyping services for academic institutions or for private companies.
Proper citation: Laragen (RRID:SCR_010989) Copy
http://www.scienceexchange.com/facilities/rutgers-university
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 3rd, 2022.
Proper citation: Rutgers University Labs and Facilities (RRID:SCR_010990) Copy
https://app.scientist.com/providers/stamford-bioprocess-technologies
Located in Southern California, USA, Stamford Bioprocess Technologies provides bioprocess and related services for recombinant protein production.
Proper citation: Stamford Bioprocess Technologies (RRID:SCR_010992) Copy
http://www.spiralgenetics.com/
Core facility which provides assistance in statistical analyses as well as in organization. Core facility offers two main analysis programs titled Spiral Genetics' BioGraph and Structural Variant Analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Spiral Genetics Incorporated (RRID:SCR_011048) Copy
http://www.scienceexchange.com/facilities/iowa-state-university
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 3rd, 2022.
Proper citation: Iowa State University Labs and Facilities (RRID:SCR_011052) Copy
https://sites.google.com/site/oncosnp/
An analytical software tool for characterizing copy number alterations and loss-of-heterozygosity (LOH) events in cancer samples from SNP genotyping data.
Proper citation: OncoSNP (RRID:SCR_012985) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/RLMM.html
A Genotype Calling Algorithm for Affymetrix SNP Arrays.
Proper citation: RLMM (RRID:SCR_012984) Copy
http://www.zebrafinchatlas.org
Expression atlas of in situ hybridization images from large collection of genes expressed in brain of adult male zebra finches. Goal of ZEBrA project is to develop publicly available on-line digital atlas that documents expression of large collection of genes within brain of adult male zebra finches.
Proper citation: Zebra Finch Expression Brain Atlas (RRID:SCR_012988) Copy
http://sourceforge.net/projects/ibdld/
A C++ software program for multipoint IBD estimation based on high density SNP genotype data.
Proper citation: IBDLD (RRID:SCR_013043) Copy
http://sourceforge.net/projects/solsnp/
A Java-based DNA variant calling tool for Next-Generation Sequencing alignment data.
Proper citation: SolSNP (RRID:SCR_013045) Copy
http://sourceforge.net/projects/tumorhats/
A software tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data.
Proper citation: HATS (RRID:SCR_013044) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/charm.html
Software package that implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol.
Proper citation: charm (RRID:SCR_012992) Copy
http://sourceforge.net/projects/chipotle-perl/
A peak-finding algorithm used to analyze ChIP-chip microarray data.
Proper citation: ChIPOTle Peak Finder (RRID:SCR_012991) Copy
http://rnaseq-mats.sourceforge.net/
Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user defined threshold. Can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design.
Proper citation: Multivariate Analysis of Transcript Splicing (RRID:SCR_013049) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/BiSeq.html
Software package that provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data.
Proper citation: BiSeq (RRID:SCR_012993) Copy
http://trinityrnaseq.sourceforge.net/
Software for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
Proper citation: Trinity (RRID:SCR_013048) Copy
http://sourceforge.net/projects/ngspeanalysis/
A pipeline using open-source tools which can implement a set of pair ended Next-generation sequencing analysis, include short reads alignment, high-quality variation genotype calling and variants annotation.
Proper citation: NGSpeAnalysis (RRID:SCR_013040) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/MEDME.html
Software that allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments.
Proper citation: MEDME (RRID:SCR_012995) Copy
https://github.com/brentp/methylcode
A single program that takes of bisulfite-treated reads and outputs per-base methylation data.
Proper citation: MethylCoder (RRID:SCR_012997) Copy
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