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http://www.bioconductor.org/packages/2.12/bioc/html/RankProd.html
Software using a non-parametric method for identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false predictions (pfp).
Proper citation: RankProd (RRID:SCR_013046) Copy
http://sourceforge.net/projects/nxgview/
A virtual software pipeline that contains several PERL modules for processing next generation sequencing data.
Proper citation: NxGview (RRID:SCR_012994) Copy
http://sourceforge.net/projects/bamformatics/
Software that provides a coherent and consistent approach to analysis of high-throughput sequencing data.
Proper citation: Bamformatics (RRID:SCR_013041) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/MEDIPS.html
Software developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq).
Proper citation: MEDIPS (RRID:SCR_012996) Copy
http://sourceforge.net/projects/bsmapper/
Sequence mapper for bisulfite sequencing reads for DNA methylation studies.
Proper citation: BSmapper (RRID:SCR_012998) Copy
http://sourceforge.net/projects/mendelscan/
A software tool for prioritizing candidate variants in family-based studies of inherited disease.
Proper citation: MendelScan (RRID:SCR_013053) Copy
http://mathgen.stats.ox.ac.uk/impute/impute_v2.html
A computer program for phasing observed genotypes and imputing missing genotypes.
Proper citation: IMPUTE2 (RRID:SCR_013055) Copy
http://compbio.bccrc.ca/software/snvmix/
Software designed to detect single nucleotide variants from next generation sequencing data.
Proper citation: SNVMix (RRID:SCR_013050) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/TurboNorm.html
Software providing a fast scatterplot smoother suitable for microarray normalization based on B-splines with second-order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available.
Proper citation: TurboNorm (RRID:SCR_012963) Copy
http://sourceforge.net/projects/probeselect/
Software for selecting probes in heterogenous transcriptional sets.
Proper citation: ProbeSelect (RRID:SCR_012965) Copy
http://sourceforge.net/projects/seqgenomebrowse/
Mini cross-platform local genome browser software designed for visualizing next-generation sequencing data.
Proper citation: SeqGenome Browser (RRID:SCR_012970) Copy
http://gmod.org/wiki/GBrowse_syn
A GBrowse-based synteny browser designed to display multiple genomes, with a central reference species compared to two or more additional species.
Proper citation: GBrowse syn (RRID:SCR_012971) Copy
http://sourceforge.net/projects/mirdp/
A computational tool for analyzing the microRNA (miRNA) transcriptome in plants.
Proper citation: miRDeep-P (RRID:SCR_013026) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/Ringo.html
Software package that facilitates the primary analysis of ChIP-chip data.
Proper citation: Ringo (RRID:SCR_012973) Copy
http://www.ebi.ac.uk/ena/about/cram_toolkit
A framework technology comprising file format and toolkit in which we combine highly efficient and tunable reference-based compression of sequence data with a data format that is directly available for computational use.
Proper citation: CRAM (RRID:SCR_012975) Copy
http://sourceforge.net/projects/quicktsaf/
Tool that compresses and decompresses fastq files.
Proper citation: KungFq (RRID:SCR_012979) Copy
http://sourceforge.net/projects/ncproseq/
Software that aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions.
Proper citation: ncPRO-seq (RRID:SCR_013031) Copy
http://sourceforge.net/projects/vcf2msat/
A python software program to identify microsatellite repeat regions based on known polymorphisms identified in a .vcf report after using SAMtools to analyze next-generation sequencing files.
Proper citation: vcf2MSAT (RRID:SCR_013034) Copy
http://sourceforge.net/projects/fishingcnv/
A software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data.
Proper citation: FishingCNV (RRID:SCR_013038) Copy
http://sourceforge.net/projects/msaprobs/
An open-source protein multiple sequence ailgnment algorithm, achieving the stastistically highest alignment accuracy on popular benchmarks.
Proper citation: MSAProbs (RRID:SCR_012982) Copy
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