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http://roadmapepigenomics.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 11, 2022. Project for human epigenomic data from experimental pipelines built around next-generation sequencing technologies to map DNA methylation, histone modifications, chromatin accessibility and small RNA transcripts in stem cells and primary ex vivo tissues selected to represent normal counterparts of tissues and organ systems frequently involved in human disease. Consortium expects to deliver collection of normal epigenomes that will provide framework or reference for comparison and integration within broad array of future studies. Consortium is also committed to development, standardization and dissemination of protocols, reagents and analytical tools to enable research community to utilize, integrate and expand upon this body of data.

Proper citation: Roadmap Epigenomics Project (RRID:SCR_008924) Copy   

•   Source: SciCrunch Registry

http://www.gzip.org/

A compression utility designed to be a replacement for compress.

Proper citation: Gzip (RRID:SCR_009291) Copy   

•   Source: SciCrunch Registry

http://bioinfo.au.tsinghua.edu.cn/software/seqsaw/

A package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data.

Proper citation: SeqSaw (RRID:SCR_009185) Copy   

•   Source: SciCrunch Registry

http://www.medinfopoli.polimi.it/GAAS/

An integrated software framework for efficient management, analysis and visualization of large amounts of gene expression data across replicated experiments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GAAS (RRID:SCR_008967) Copy   

•   Source: SciCrunch Registry

http://metagenomics.atc.tcs.com/compression/DELIMINATE/

A practical implementation of a novel compression approach that can rapidly compress FASTA files containing genomic sequence data in a loss-less fashion.

Proper citation: DELIMINATE (RRID:SCR_008956) Copy   

•   Source: SciCrunch Registry

https://gmod.org/wiki/CMap.1

Web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. (entry from Genetic Analysis Software)

Proper citation: CMAP (RRID:SCR_009034) Copy   

•   Source: SciCrunch Registry

http://www.ics.uci.edu/~dnazip/

DNA sequence compression using a reference genome.

Proper citation: DNAzip (RRID:SCR_009032) Copy   

•   Source: SciCrunch Registry

http://www.ufrgs.br/RNAi/isomiRID/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on 4/1/14. Software providing a framework to find isomiRNAs, templated and non-templated modifications in microRNAs.

Proper citation: isomiRID (RRID:SCR_009809) Copy   

•   Source: SciCrunch Registry

http://mocklerlab.org/tools/1

An application for discovering potential splice junctions in high throughput sequencing (HTS) data.

Proper citation: Supersplat (RRID:SCR_009826) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/popoolationte/

A quick and simple pipeline for the analysis of transposable element (TE) insertions in (natural) populations using next generation sequencing. It calculates TE insertion frequencies for TEs that are present in the reference genome as well as for novel TE insertions. PoPoolation TE requires paired-end reads from a pooled population, a reference sequence and transposable element sequences (fasta-file).

Proper citation: PoPoolation TE (RRID:SCR_005131) Copy   

•   Source: SciCrunch Registry

http://en.bioinformatica-na-escola.org/

Project to use bioinformatics-based research activities in high schools that provides teachers and students training materials to support the teaching of Life Sciences, particularly in the area of Biology. Their aims include new ways to learn biology, adapting Bioinformatics exercises to the curricula of practical classes, and encouraging the acquisition of new scientific and technological knowledge.

Proper citation: Bioinformatics(at)school (RRID:SCR_005245) Copy   

•   Source: SciCrunch Registry

http://woldlab.caltech.edu/rnaseq

Software for Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq. Its functions are to (i) assign reads that map uniquely in the genome to their site of origin and, for reads that match equally well to several sites (''multireads''), assign them to their most likely site(s) of origin; (ii) detect splice-crossing reads and assign them to their gene of origin; (iii) organize reads that cluster together, but do not map to an already known exon, into candidate exons or parts of exons; and (iv) calculate the prevalence of transcripts from each known or newly proposed RNA, based on normalized counts of unique reads, spliced reads and multireads. The new candidate RNA regions produced can be thought of as ESTs, and, like ESTs, some are provisionally appended to existing gene models if they meet several additional criteria. Remaining unassigned candidate transcribed regions (labeled RNAFAR features) can then be used in conjunction with other confirming data to develop new or revised gene models.

Proper citation: ERANGE (RRID:SCR_005240) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/cancer/cga/rna-seqc

Java software which computes a series of quality control metrics for RNA-seq data and can compare sequencing quality across different samples or experiments to evaluate different experimental parameters. The input can be one or more BAM files, and the output consists of HTML reports and tab delimited files of metrics data.

Proper citation: RNA-SeQC (RRID:SCR_005120) Copy   

•   Source: SciCrunch Registry

http://www.nature.com/naturejobs/science/

Search for the widest range of science jobs with thousands of vacancies advertised globally on the site. Employers range from top international pharmaceutical and biotechnology companies to highly respected academic and government institutions. Job seekers can find a wide range of scientific career information and news as well as expert advice, all free to access. What''s more, employers can post jobs for free.

Proper citation: Naturejobs (RRID:SCR_005151) Copy   

•   Source: SciCrunch Registry

http://www.jobs.ac.uk/

International job board for careers in academic, research, science and related professions in the UK, Europe, Australasia, Africa, America and Asia & Middle East. Launched by the University of Warwick, they have grown to become the top recruitment site in their sector, attracting the most qualified and talented people from the UK, Europe and across the world. Users may subscribe to Jobs by Email for vacancies in universities, colleges, research institutions, commercial and public sector, schools and charities. You may upload your CV to give yourself an advantage by making your CV visible to top employers now!

Proper citation: jobs.ac.uk (RRID:SCR_005154) Copy   

•   Source: SciCrunch Registry

http://www.pantherdb.org/tools/csnpScoreForm.jsp

Data analysis service that estimates the likelihood of a particular nonsynonymous (amino-acid changing) coding SNP to cause a functional impact on the protein. To analyze many SNPs, download the PANTHER Coding Snp Analysis tool from the downloads page.

Proper citation: PANTHER Evolutionary analysis of coding SNPs (RRID:SCR_005145) Copy   

•   Source: SciCrunch Registry

http://www.cmbi.ru.nl/hope/home

An easy-to-use webserver that analyses the structural effects of your mutation of interest. The server allows you to submit a protein sequence and the mutation. Project HOPE will then collect and combine available information from a series of webservers and databases and will produce a mutation report complete with results, figures and animations. Where available Project HOPE will use the 3D structure of the protein but the server can also build a homology model if necessary. Other information sources include the Uniprot database and a series of DAS prediction servers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Project HOPE (RRID:SCR_005141) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/methylkit/

An R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: methylKit (RRID:SCR_005177) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/gesnd/

A software package and a pipeline for identifying causal mutations for rare congenital diseases by next-generation sequencing. Features * one-stop solution for identifying causal mutations of rare genetic diseases * detect wide-spctrum variants, including medium and large sized indels, and tandem repeats * annotate and filter variants * prioritize candidate variants

Proper citation: GESND (RRID:SCR_005179) Copy   

•   Source: SciCrunch Registry

http://www.well.ox.ac.uk/~kgaulton/chaos.shtml

A Perl-based system for annotation of variants identified in high-throughput sequencing experiments. Functionality includes annotation of variants with information relating to population genetics, known transcripts, positional records, and sequence motif-based prediction. In addition, annotated variants can be summarized and extracted to facilitate downstream analysis. There is also basic support for gene-based biological annotation, and eventually will include tools for variant and genotype analysis and visualization.

Proper citation: CHAoS (RRID:SCR_005174) Copy   

•   Source: SciCrunch Registry