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http://www.bioconductor.org/packages/devel/bioc/html/ChIPXpress.html

A R package designed to improve ChIP-seq and ChIP-chip target gene ranking using publicly available gene expression data. It takes as input predicted transcription factor (TF) bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target.

Proper citation: ChIPXpress (RRID:SCR_006653) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/softsearch/

A sensitive structural variant (SV) detection software tool for Illumina paired-end next-generation sequencing data. It simultaneously utilizes soft-clipping and read-pair strategies for detecting SVs to increase sensitivity. Soft clips are proxies for split-reads that indicate part of the read maps to the reference genome, but the other part is not localized at the same place (e.g. breakpoint spanning reads). Discordant read-pairs refer to a read and its mate, where the insert size is greater (or less than) the expected distribution of the dataset ? or ? where the mapping orientation of the reads is unexpected (e.g. both on the same strand). SoftSearch looks for areas with soft-clipping in the genome that have discordant read pairs supporting the anomaly. Once areas with both these conditions are identified, the read and mate information is extracted directly from the BAM file containing the discordant reads, obviating the need for time-consuming and error-prone complex alignment strategies. Only a small number of soft-masked bases discordant read-pairs are necessary to identify an SV, which on their own would not be sufficient to make an SV call, thus highlighting SoftSearch?s improved sensitivity. SoftSearch is well suited to be ?plugged in? to most sequence analysis workflows, since it requires standard file inputs, such as a BAM file using almost any aligner and a reference genome FASTA file. Because SoftSearch requires soft-masked bases, the only requirement is that the aligner must have this functionality, which is usually turned on by default by many standard aligners (e.g. BWA, Novoalign, etc).

Proper citation: SoftSearch (RRID:SCR_006683) Copy   

•   Source: SciCrunch Registry

http://watson.nci.nih.gov/bioc_mirror/packages/2.11/bioc/html/EDASeq.html

Software for numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: EDASeq (RRID:SCR_006751) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.pims-lims.org/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://bioviz.org/igb/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.synbrowse.org/

A generic sequence comparison tool for visualizing genome alignments both within and between species.

Proper citation: SynBrowse (RRID:SCR_011807) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/condetri/

Software tool as content dependent read trimmer for Illumina data. Content dependent read trimming software for Illumina/Solexa sequencing data.

Proper citation: ConDeTri (RRID:SCR_011838) Copy   

•   Source: SciCrunch Registry

http://www.cbcb.umd.edu/software/quake/

A software package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads.

Proper citation: Quake (RRID:SCR_011839) Copy   

•   Source: SciCrunch Registry

http://www.sbeams.org/

Software providing a framework for collecting, storing, and accessing data produced by a wide variety of experiments.

Proper citation: SBEAMS (RRID:SCR_011830) Copy   

•   Source: SciCrunch Registry

http://circos.ca/

A software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.

Proper citation: Circos (RRID:SCR_011798) Copy   

•   Source: SciCrunch Registry

http://www.h-invitational.jp/g-compass/

It visualizes evolutionarily conserved genomic regions between human and other 12 vertebrates based on original genome alignments pursuing higher coverage.

Proper citation: G-compass (RRID:SCR_011799) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/discovering-cse/

Software for discovering motifs that induce sequencing errors.

Proper citation: discovering-cse (RRID:SCR_011832) Copy   

•   Source: SciCrunch Registry