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http://sourceforge.net/projects/abmining/
Python scripts to analyze antibody libraries sequenced by next generation sequencing methods (454, Ion Torrent, MiSeq).
Proper citation: AbMining ToolBox (RRID:SCR_000090) Copy
https://code.google.com/p/snavi/
Desktop application for analysis and visualization of large-scale cell signaling networks.
Proper citation: SNAVI (RRID:SCR_000091) Copy
http://docking.sce.ntu.edu.sg/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Web service that is used by researchers and scientists to perform protein-ligand covalent docking. This form allows for the formation of covalent linkages between the ligand and the receptor.
Proper citation: CovalentDock Cloud (RRID:SCR_000126) Copy
http://sourceforge.net/projects/spdesigner/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An open source software program for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa.
Proper citation: SP-Designer (RRID:SCR_000031) Copy
https://github.com/brendanofallon/SNPSVM/
A support vector machine for calling variants from next-gen sequencing data. It takes as input a BAM-formatted alignment of sequencing reads, and emits a VCF formatted file describing where all the SNPs (single nucleotide polymorphisms) are.
Proper citation: SNPSVM (RRID:SCR_000028) Copy
https://code.google.com/p/ghostm/
Software homology search tool for huge short reads generated by next-generation sequencers.Can detect remote homologs like BLAST and is about 40 times more efficient than BLAST by using a GPU-computing technique.
Proper citation: GHOSTM (RRID:SCR_000062) Copy
https://code.google.com/p/primer-design/
An open-source C++ software library of classes for the design and analysis of primers suitable for a wide range of PCR applications.
Proper citation: PD5 (RRID:SCR_000068) Copy
http://sourceforge.net/projects/mysirna/
Software that integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches.
Proper citation: MysiRNA-designer (RRID:SCR_000102) Copy
http://www.ngsbicocca.org/html/fusion_analyser.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2023. Software used to detect gene fusions from paired-end RNA-Seq data.
Proper citation: Fusion Analyser (RRID:SCR_000059) Copy
http://bioconductor.org/packages/release/bioc/html/CorMut.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software package for computing correlated mutations based on selection pressure. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network.
Proper citation: CorMut (RRID:SCR_000053) Copy
http://www.bioconductor.org/packages/release/bioc/html/metaSeq.html
Software package for meta-analysis of RNA-Seq count data in multiple studies. The probabilities by one-sided NOISeq are combined by Fisher's method or Stouffer's method.
Proper citation: metaSeq (RRID:SCR_000056) 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
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://jexpress.bioinfo.no/site/
Gene expression analysis software using Java.
Proper citation: J-Express (RRID:SCR_003609) 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
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