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http://www.genabel.org/packages/MetABEL
Software for meta-analysis of genome-wide SNP association results.
Proper citation: MetABEL (RRID:SCR_003429) Copy
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
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
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://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
http://sourceforge.net/projects/insertionmapper/
A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. It consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution and Element Mapping. This pipeline tool is applicable to scenarios requiring analysis of the tremendous output of short reads produced in NGS sequencing experiments of targeted genome sequences.
Proper citation: InsertionMapper (RRID:SCR_004163) 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
http://genome.gsc.riken.jp/osc/english/dataresource/
A program to eliminate artifactual reads from next-generation sequencing data sets.
Proper citation: TagDust (RRID:SCR_004175) Copy
https://www.hgsc.bcm.edu/software/mercury
An automated, flexible, and extensible analysis workflow that provides accurate and reproducible genomic results at scales ranging from individuals to large cohorts. The analysis pipeline is deployed in local hardware and the Amazon Web Services cloud via the DNAnexus platform.
Proper citation: Mercury (RRID:SCR_004231) Copy
http://cb-commander.sourceforge.net/pmwiki.php
A plugin based software tool that tries to integrate high throughput sequencing algorithms. It allows researchers to design and execute their experiments through a user friendly interface, enabling users to integrate di erent components of an experiment, e.g. algorithms and converters, into one graphically interfaced application that is very easy to use when working on remote servers as well as local computers. The graphical user interface facilitates a visual design of experiments by using a block diagram to represent the components (algorithms, converters, etc.) of an experiment as a pipeline. The users can easily modify this pipeline.
Proper citation: CB-Commander (RRID:SCR_004237) Copy
http://www.sanger.ac.uk/resources/software/artemis/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Free genome browser and annotation tool that allows visualization of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Artemis is free software and is distributed under the terms of the GNU General Public License. Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.
Proper citation: Artemis: Genome Browser and Annotation Tool (RRID:SCR_004267) Copy
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