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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.bioconductor.org/packages/release/bioc/html/eisa.html
A biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular) data.
Proper citation: eisa (RRID:SCR_012883) Copy
http://sourceforge.net/projects/trowel-ec/
An error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach.
Proper citation: Trowel (RRID:SCR_012890) Copy
http://bioconductor.org/packages/release/bioc/html/CSAR.html
Statistical tools for the analysis of ChIP-seq data.
Proper citation: CSAR (RRID:SCR_012930) Copy
https://github.com/jstjohn/SeqPrep
A program to merge paired end Illumina reads that are overlapping into a single longer read.
Proper citation: SeqPrep (RRID:SCR_013004) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/phyloseq.html
Software for handling and analysis of high-throughput microbiome census data.
Proper citation: phyloseq (RRID:SCR_013080) Copy
http://sourceforge.net/projects/amos/
A collection of tools and class interfaces for the assembly of DNA reads.
Proper citation: AMOS (RRID:SCR_013067) Copy
http://aluru-sun.ece.iastate.edu/doku.php?id=reptile
A software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing platforms.
Proper citation: Reptile (RRID:SCR_013075) Copy
http://microbiomeutil.sourceforge.net/#A_CS
A chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp).
Proper citation: ChimeraSlayer (RRID:SCR_013283) Copy
http://sourceforge.net/projects/telescoper/
An algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework.
Proper citation: Telescoper (RRID:SCR_013206) Copy
http://alumni.cs.ucr.edu/~liw/isolasso.html
An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.
Proper citation: IsoLasso (RRID:SCR_013176) Copy
http://sourceforge.net/projects/heuraa/
Software for accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.
Proper citation: HeurAA (RRID:SCR_013212) Copy
https://sites.google.com/site/quantisnp/
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.Software to detect rare or de novo copy number alterations in normal DNA samples. Please note that QuantiSNP is no longer under active development.
Proper citation: QuantiSNP (RRID:SCR_013091) Copy
http://bioinfo.ctb.pku.edu.cn/MAP/
This resource is out of service. Documented on February 23,2021. Software for de novo metagenomic assembly program for shotgun DNA reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MAP (RRID:SCR_013216) Copy
http://bowtie-bio.sourceforge.net/crossbow/index.shtml
A scalable software pipeline for whole genome resequencing analysis.
Proper citation: Crossbow (RRID:SCR_013306) Copy
http://tomcatbackup.esat.kuleuven.be/inclusive/
A suit of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.
Proper citation: INCLUSive (RRID:SCR_013488) Copy
http://hannonlab.cshl.edu/Alta-Cyclic/main.html
An Illumina Genome-Analyzer (Solexa) base caller.
Proper citation: Alta-Cyclic (RRID:SCR_013373) Copy
https://omics.pnl.gov/software/ms-gf
Software that performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
Proper citation: MS-GF+ (RRID:SCR_015646) Copy
American multinational technology company that specializes in internet related services and products, which include online advertising technologies, search engine, cloud computing, software, and hardware. Considered one of Big Four technology companies, alongside Amazon, Apple and Facebook.
Proper citation: Google (RRID:SCR_017097) Copy
https://github.com/HIITMetagenomics/dsm-framework
Software package providing distributed string mining for High-Throughput Sequencing data that provides a content-based exploration and retrieval method for whole metagenome sequencing samples.
Proper citation: Distributed String Mining Framework (RRID:SCR_004736) Copy
https://tobiasrausch.com/delly/
Integrated structural variant prediction software that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout genome.
Proper citation: DELLY (RRID:SCR_004603) Copy
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