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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.partek.com/?q=partekgs
A comprehensive suite of advanced statistics and interactive data visualization specifically designed to reliably extract biological signals from noisy data.
Proper citation: Partek Genomics Suite (RRID:SCR_011860) Copy
http://sbcb.bioch.ox.ac.uk/cgdb/
A database of membrane protein/lipid interactions by coarse-grained molecular dynamics simulations.
Proper citation: CGDB (RRID:SCR_011959) Copy
http://www.clcbio.com/clc-plugin/duplicate-reads-removal-plugin/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Plug-in tool to filter out duplicate reads that is specifically well-suited to handle those coming from PCR amplification errors which can have a negative effect because a certain sequence is represented in artificially high numbers.
Proper citation: Duplicate reads removal (RRID:SCR_000231) Copy
Software to address all aspects of Next Generation Sequencing data workflow.
Proper citation: Lab7 (RRID:SCR_001210) Copy
An optional module in the Omixon Target application suite for HLA typing using NGS (next-generation sequencing) data that gives high resolution results with whole genome, exome or very targeted DNA data, or with RNA seq data.
Proper citation: Omixon Target HLA Typing (RRID:SCR_001206) Copy
http://www.goldenhelix.com/SNP_Variation/SNP_Analysis_Package/index.html
SNP Analysis software for basic to advanced analyses that incorporates a number of intuitive workflows to lead you beyond single marker associations. With support for case-control and quantitative traits, whole genome and candidate gene data, you can run a breadth of statistical tests under several genetic models. Advanced regression can further help elucidate even the most complex gene-gene and gene-environment interactions.
Proper citation: SNP and Variation Suite SNP Analysis (RRID:SCR_001285) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Sequence analysis software for molecular biologists.
Proper citation: VectorFriends (RRID:SCR_001230) Copy
http://www.spiralgenetics.com/products/
Analysis pipeline that accurately detects and maps variations that are often missed by standard analysis algorithms. It uses direct de novo read overlap assembly to accurately detect and characterize SNPs (single nucleotide polymorphisms), indels, and SVs (structural variations). The pipeline uses existing Illumina HiSeq data and does not require additional library preparation. The algorithm is optimized for projects with at least 20x coverage per chromosome set (i.e. 40x for diploid).
Proper citation: Anchored Assembly (RRID:SCR_001188) Copy
https://www.integromics.com/omicsoffice-for-ngs/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software for secondary and tertiary analysis of Next Generation Sequencing (NGS) data.
Proper citation: OmicsOffice for NGS SeqSolve (RRID:SCR_001222) Copy
https://github.com/epigenomics/methylmaps
A data analysis pipeline for the Methyl-MAPS method.
Proper citation: Methyl-Analyzer (RRID:SCR_000318) Copy
https://www.infoquant.com/cghfusion
Software for DNA Copy Number and loss of heterozygosity (LOH) analysis designed with high-throughput diagnostic laboratories in mind.
Proper citation: CGH Fusion (RRID:SCR_000295) Copy
https://github.com/hmsiccbl/screensaver
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for a Lab Information Management System (LIMS) for high-throughput screening of small molecule and RNAi biological assays.
Proper citation: Screensaver (RRID:SCR_000297) Copy
http://anya.igsb.anl.gov/Geneways/GeneWays.html
System for automatically extracting, analzying, visualizing and integrating molecular pathway data from the research literature. System focuses on interactions between molecular substances and actions, providing a graphical consensus view on the collected information. GeneWays is designed as open platform, allowing researchers to query, review and critique integrated information.
Proper citation: GeneWays (RRID:SCR_000572) Copy
http://bowtie-bio.sourceforge.net/recount/
RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward.
Proper citation: ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) Copy
http://www.bioinfor.com/zoom/general/overview.html
Software to map the Illumina/Solexa reads of 15x coverage of a human genome to the reference human genome in one CPU-day, allowing two mismatches, at full sensitivity.
Proper citation: ZOOM (RRID:SCR_002175) Copy
http://www.biogazelle.com/qbaseplus
Software program for quantitative PCR (qPCR) data analysis based on geNorm and qBase technology.
Proper citation: qBasePLUS (RRID:SCR_003370) Copy
https://github.com/neufeld/pandaseq
Software program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
Proper citation: PANDAseq (RRID:SCR_002705) Copy
http://primerdigital.com/fastpcr.html
Software tool for PCR primers or probe design, in silico PCR, oligonucleotide assembly and analyses, alignment and repeat searching.
Proper citation: FastPCR (RRID:SCR_003155) Copy
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