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https://github.com/dbitton/LaSSO
An R script that creates a FASTA database containing all possible lariat signatures from a given set of introns.
Proper citation: LaSSO (RRID:SCR_003418) Copy
http://www.metafor-project.org/doku.php
A free and open-source add-on for conducting meta-analyses with the statistical software environment R.
Proper citation: metaphor (RRID:SCR_003450) Copy
Database of protein families and domains that is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. ScanProsite finds matches of your protein sequences to PROSITE signatures. PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains. Each of these signatures comes with documentation providing background information on the structure and function of these proteins. The database is available via FTP.
Proper citation: PROSITE (RRID:SCR_003457) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/minfi.html
Software that improves the results from the Illumina infinium HumanMethylation450 BeadChips by reducing technical variation within and between arrays. SWAN is available in the minfi Bioconductor package.
Proper citation: SWAN (RRID:SCR_003455) Copy
https://code.google.com/p/bmiq/
Software using a beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data.
Proper citation: BMIQ (RRID:SCR_003446) Copy
A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context.
Proper citation: GEPAT (RRID:SCR_003597) Copy
http://jexpress.bioinfo.no/site/
Gene expression analysis software using Java.
Proper citation: J-Express (RRID:SCR_003609) Copy
Oligonucleotide design software that calculates optimal oligonucleotides for a range of tasks: sequence assembly, differential expression, and microarrays (cDNA and spotted oligos)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Osprey (RRID:SCR_003627) Copy
http://srna-tools.cmp.uea.ac.uk/
Software tools for the analysis of high-throughput small RNA data.
Proper citation: UEA sRNA toolkit (RRID:SCR_003620) Copy
http://khavarilab.stanford.edu/resources.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. An intersection-based pathogen detection workflow that utilizes a user-provided custom reference genome set for identification of nonhuman sequences in deep sequencing datasets. This is a package recommended for advanced users only.
Proper citation: RINS (RRID:SCR_003652) Copy
http://malde.org/~ketil/jatac/sources/
Software program for filtering duplicate 454 sequences by comparing flowgram information.
Proper citation: JATAC (RRID:SCR_003978) Copy
http://www.antibodyresource.com/
A complete guide to antibody research and suppliers. Serving the scientific community since 1997, the Antibody Resource Page is a guide designed by scientists for scientists to find companies that sell catalog antibodies and custom monoclonal and polyclonal antibodies. See our other pages on antibody-related databases, software, and educational websites. If you wish to suggest or update a link, please see our FAQ.
Proper citation: Antibody Resource Page (RRID:SCR_004069) Copy
http://mendel.stanford.edu/sidowlab/downloads/quest/
A Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitation (ChIP-seq) experiments.
Proper citation: Quantitative Enrichment of Sequence Tags (RRID:SCR_004065) Copy
http://www.brl.bcm.tmc.edu/pash/pashDownload.rhtml
Performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing.
Proper citation: Pash 3.0 (RRID:SCR_004078) Copy
http://epigraph.mpi-inf.mpg.de/WebGRAPH/
A software for genome and epigenome analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: EpiGRAPH (RRID:SCR_004326) Copy
https://bcbio-nextgen.readthedocs.org/en/latest/
A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis.
Proper citation: bcbio-nextgen (RRID:SCR_004316) Copy
https://github.com/dsturg/Spanki
A set of tools to facilitate analysis of alternative splicing from RNA-SEQ data.
Proper citation: Spanki (RRID:SCR_004469) Copy
http://sourceforge.net/projects/pasha/
A parallel short read assembler for large genomes using de Bruijn graphs.
Proper citation: PASHA (RRID:SCR_004455) Copy
http://www.leonxie.com/DeepFinder.php
Provides an comprehensive workflow of analyzing data from plant microRNA (miRNA) deep sequencing.
Proper citation: miRDeepFinder (RRID:SCR_004456) Copy
http://virome.diagcomputing.org/#view=home
A web-application designed for scientific exploration of metagenome sequence data collected from viral assemblages occurring within a number of different environmental contexts. The VIROME informatics pipeline focuses on the classification of predicted open-reading frames (ORFs) from viral metagenomes. The portal allows you to submit your viral metagenome to be processed through the VIROME analysis pipeline, and enable you to investigate your data via the VIROME user interface., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: VIROME (RRID:SCR_004362) Copy
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