Tools   Select Another Resource Report Type

http://prodom.prabi.fr/

Comprehensive set of protein domain families automatically generated from UniProt Knowledge Database. Automated clustering of homologous domains generated from global comparison of all available protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ProDom (RRID:SCR_006969) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/2.9/bioc/html/RamiGO.html

Software package with an R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape.

Proper citation: RamiGO (RRID:SCR_006922) Copy   

•   Source: SciCrunch Registry

http://www.seqan.de/projects/razers/

A read mapping software program with adjustable sensitivity based on counting q-grams. RazerS 3 supports shared-memory parallelism, an additional seed-based filter with adjustable sensitivity, a much faster, banded version of the Myers? bit-vector algorithm for verification, memory saving measures and support for the SAM output format. This leads to a much improved performance for mapping reads, in particular long reads with many errors.

Proper citation: RazerS (RRID:SCR_006889) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/crop-tingchenlab/

A clustering tool designed mainly for Metagenomics studies, which clusters 16S rRNA sequences into Operational Taxonomic Units (OTU). By using a Gaussian Mixture model, CROP can automatically determine the best clustering result for 16S rRNA sequences at different phylogenetic levels without setting a hard cutoff threshold as hierarchical clustering does. Yet, at the same time, it is able to manage large datasets and to overcome sequencing errors.

Proper citation: CROP (RRID:SCR_006916) Copy   

•   Source: SciCrunch Registry

http://math.mcb.berkeley.edu/~meromit/MetMap/

A computational pipeline for the analysis of MethylSeq experiments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MetMap (RRID:SCR_006954) Copy   

•   Source: SciCrunch Registry

http://bowtie-bio.sourceforge.net/myrna/index.shtml

A cloud computing tool for calculating differential gene expression in large RNA-seq datasets. It uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization, and statistical testing. These tools are combined in an automatic, parallel pipeline that runs in the cloud (Elastic MapReduce in this case) on a local Hadoop cluster, or on a single computer, exploiting multiple computers and CPUs wherever possible.

Proper citation: Myrna (RRID:SCR_006951) Copy   

•   Source: SciCrunch Registry

https://github.com/jstjohn/SimSeq

An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries .

Proper citation: SimSeq (RRID:SCR_006947) Copy   

•   Source: SciCrunch Registry

http://www.cancergenomics.org/

Consortium promoting communication and collaboration among cancer cytogenomics laboratories, who are interested in applying microarray technologies to cancer diagnosis and cancer research. Their oals are to (1) establish platform-neutral and cancer specific microarray designs for diagnostic purposes, (2) share cancer microarray data between participating institutions for education purposes, (3) create a public cancer array database, and (4) carry out multicenter cancer genome translational research. Collaboration amongst the different laboratories and researchers will not only provide validation for the microarray design(s) but ultimately provide more comprehensive molecular information and more accurate interpretation to better serve cancer patients and further cancer research. The CGC was officially incorporated in June 2010 as a not-for-profit organization.

Proper citation: Cancer Genomics Consortium (RRID:SCR_002384) Copy   

•   Source: SciCrunch Registry

http://www.clsi.org/

A not-for-profit membership organization that brings together the global laboratory community to foster excellence in laboratory medicine by facilitating the development of clinical laboratory testing standards based on input from and consensus among industry, government, and health care professionals. CLSI is setting the standard for quality in clinical laboratory testing around the world.

Proper citation: Clinical and Laboratory Standards Institute (RRID:SCR_002382) Copy   

•   Source: SciCrunch Registry

http://www.statmethods.net/index.html

Training material created for both current R users, and experienced users of other statistical packages (e.g., SAS, SPSS, Stata) who would like to transition to R to help you quickly access this language in your work. The book inspired by this site takes the material here and significantly expands upon it.

Proper citation: Quick-R (RRID:SCR_002417) Copy   

•   Source: SciCrunch Registry

http://128.32.118.212/thorfinn/realSFS/

Software program used to estimate allele frequency and SNP calling., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: realSFS (RRID:SCR_002493) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowBeads.html

Software package for the analysis of flow cytometry bead data. It extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalization.

Proper citation: flowBeads (RRID:SCR_002440) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowCyBar.html

A software package to analyze flow cytometric data using gate information to follow population / community dynamics.

Proper citation: flowCyBar (RRID:SCR_002319) Copy   

•   Source: SciCrunch Registry

http://www.r-tutor.com/

Couple of introductory tutorials on basic R concepts that provides an introduction to the R programming language, and illustrates its use by solving elementary statistics textbook exercises. Beyond the basics, they also cover topics of GPU computing in R. An R Tutorial eBook is also available.

Proper citation: R Tutorial - An R Introduction to Statistics (RRID:SCR_002394) Copy   

•   Source: SciCrunch Registry

https://github.com/nh13/DWGSIM

Whole Genome Simulator for Next-Generation Sequencing.

Proper citation: DWGSIM (RRID:SCR_002342) Copy   

•   Source: SciCrunch Registry

https://github.com/BEETL/BEETL

Software tool that not only compresses FASTQ-formatted DNA reads more compactly than gzip but also permits rapid search for k-mer queries within the archived sequences. The full FASTQ record of each matching read or read pair is returned, allowing the search results to be piped directly to any of the many standard tools that accept FASTQ data as input. Searchable compressed archive for DNA reads.

Proper citation: BEETL-fastq (RRID:SCR_002341) Copy   

•   Source: SciCrunch Registry

https://github.com/PhKoch/RepARK

Software using a de novo repeat assembly method which avoids potential biases by using abundant k-mers of next-generation sequencing (NGS) whole genome sequencing (WGS) reads without requiring a reference genome.

Proper citation: RepARK (RRID:SCR_002333) Copy   

•   Source: SciCrunch Registry

http://www.thermofisher.com/order/catalog/product/4385261

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 28, 2017.

Software that performs comparative sequencing, also known as direct sequencing, medical sequencing, PCR sequencing and resequencing with DNA sequencing files. The software is designed for reference based and non-reference based analysis such as mutation detection and analysis, SNP discovery and validation and sequence confirmation.

Proper citation: Variant Reporter Software (RRID:SCR_002329) Copy   

•   Source: SciCrunch Registry

http://www.ddbj.nig.ac.jp

Maintains and provides archival, retrieval and analytical resources for biological information. Central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: DDBJ Omics Archive and BioProject. DOR is archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides organizational framework to access metadata about research projects and data from projects that are deposited into different databases.

Proper citation: DNA DataBank of Japan (DDBJ) (RRID:SCR_002359) Copy   

•   Source: SciCrunch Registry

https://github.com/seqan/seqan/tree/master/apps/mason2

Collection of software tools for simulating biological sequences, including simulations of genome fragment sampling, random genomic sequences, methylation levels, and NGS reads.

Proper citation: Mason (RRID:SCR_002476) Copy   

•   Source: SciCrunch Registry