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http://www.bioconductor.org/packages/release/bioc/html/flowPlots.html
Software for analysis plots and data class for gated flow cytometry data.
Proper citation: flowPlots (RRID:SCR_002177) Copy
http://cran.r-project.org/web/packages/metaRNASeq/
Software package for meta-analysis of RNA-seq data. This package implements two p-value combination techniques (inverse normal and Fisher methods). It also provides a vignette explaining how to combine data from multiple RNA-seq experiments.
Proper citation: metaRNASeq (RRID:SCR_002174) Copy
https://cran.r-project.org/src/contrib/Archive/demi/
R package for estimating differential expression from multiple indicators that capitalizes on the high number of concurrent measurements. It extends to various experimental designs and target categories (transcripts, genes, genomic regions) as well as small sample sizes.
Proper citation: DEMI (RRID:SCR_002291) Copy
http://www.bioconductor.org/packages/release/bioc/html/flowCore.html
A Bioconductor software package for high throughput flow cytometry that provides S4 data structures and basic functions.
Proper citation: flowCore (RRID:SCR_002205) Copy
http://www.bioconductor.org/packages/release/bioc/html/flowBeads.html
Software package for the analysis of flow cytometry bead data. It extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalization.
Proper citation: flowBeads (RRID:SCR_002440) Copy
http://www.bioconductor.org/packages/release/bioc/html/flowCyBar.html
A software package to analyze flow cytometric data using gate information to follow population / community dynamics.
Proper citation: flowCyBar (RRID:SCR_002319) Copy
https://github.com/nh13/DWGSIM
Whole Genome Simulator for Next-Generation Sequencing.
Proper citation: DWGSIM (RRID:SCR_002342) Copy
https://github.com/BEETL/BEETL
Software tool that not only compresses FASTQ-formatted DNA reads more compactly than gzip but also permits rapid search for k-mer queries within the archived sequences. The full FASTQ record of each matching read or read pair is returned, allowing the search results to be piped directly to any of the many standard tools that accept FASTQ data as input. Searchable compressed archive for DNA reads.
Proper citation: BEETL-fastq (RRID:SCR_002341) Copy
https://github.com/PhKoch/RepARK
Software using a de novo repeat assembly method which avoids potential biases by using abundant k-mers of next-generation sequencing (NGS) whole genome sequencing (WGS) reads without requiring a reference genome.
Proper citation: RepARK (RRID:SCR_002333) Copy
http://www.raetschlab.org/suppl/palmapper
Computes both spliced and unspliced alignments at high accuracy while taking advantage of base quality information and splice site predictions.
Proper citation: PALMapper (RRID:SCR_011466) Copy
Software for a Laboratory Information Management System (LIMS) developed to support the unpredictable workflows of Molecular biology and Protein production labs of all sizes.
Proper citation: PiMS (RRID:SCR_011816) Copy
http://tron-mainz.de/tron-facilities/computational-medicine/galaxy-lims/
A laboratory information management system (LIMS) for a next-generation sequencing (NGS) laboratory within the existing Galaxy platform.
Proper citation: Galaxy LIMS (RRID:SCR_011829) Copy
http://archimedes.cheme.cmu.edu/?q=gpublast
Software for an accelerated version of the popular NCBI-BLAST using a general-purpose graphics processing unit (GPU). It s nearly four times faster, while producing identical results. GPU-BLAST supports: protein alignment according to blastp (it does not support psiblast), multiple CPU threads working in parallel with a single GPU, and input files with multiple protein queries.
Proper citation: GPU-BLAST (RRID:SCR_011820) Copy
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastx&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
A web-based tool used to search translated nucleotide databases using a translated nucleotide query.
Proper citation: TBLASTX (RRID:SCR_011823) Copy
An easy-to-use, highly customizable genome browser you can use to visualize and explore genomic data and annotations, including RNA-Seq, ChIP-Seq, tiling array data, and more.
Proper citation: IGB (RRID:SCR_011792) Copy
http://www.broadinstitute.org/igv/
A high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
Proper citation: Integrative Genomics Viewer (RRID:SCR_011793) Copy
http://www.ncbi.nlm.nih.gov/tools/gbench/
An integrated application for viewing and analyzing sequence data.
Proper citation: NCBI Genome Workbench (RRID:SCR_011794) Copy
https://code.google.com/p/ngsplot/
A software program that allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions.
Proper citation: ngs.plot (RRID:SCR_011795) Copy
http://www.cs.utah.edu/~miriah/mizbee/Overview.html
A multiscale synteny browser for exploring conservation relationships in comparative genomics data.
Proper citation: MizBee (RRID:SCR_011804) Copy
http://pipmaker.bx.psu.edu/pipmaker/
PipMaker computes alignments of similar regions in two DNA sequences. Moreover, MultiPipMaker can be requested to compute a true multiple alignment of the input sequences and return a nucleotide-level view of the results.
Proper citation: PipMaker and MultiPipMaker (RRID:SCR_011806) Copy
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