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http://www.bioconductor.org/packages/release/bioc/html/rqubic.html

This software package implements the QUBIC algorithm for the qualitative biclustering with gene expression data.

Proper citation: rqubic (RRID:SCR_012869) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/DiffBind.html

Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

Proper citation: DiffBind (RRID:SCR_012918) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/eisa.html

A biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular) data.

Proper citation: eisa (RRID:SCR_012883) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/trowel-ec/

An error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach.

Proper citation: Trowel (RRID:SCR_012890) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/CSAR.html

Statistical tools for the analysis of ChIP-seq data.

Proper citation: CSAR (RRID:SCR_012930) Copy   

•   Source: SciCrunch Registry

https://github.com/Mangul-Lab-USC/telescope

Open source web application that tracks progress of jobs submitted to remote servers using Sun Grid Engine (SGE) on-demand scheduling system. Allows remote scheduling of pre-defined pipelines, as well as re-scheduling queued jobs. Telescope does not assume anything from the remote server, except for SSH connection. The connection is established using SSH key pairs that are stored after encrypted.

Proper citation: Telescope (RRID:SCR_017626) Copy   

•   Source: SciCrunch Registry

https://laniakea-elixir-it.github.io/

Software tool for automatic deployment of virtual Galaxy environments for life science. Can be deployed over common cloud architectures supported both by public and private e-infrastructures. User interacts with Laniakea based service through simple front end that allows general setup of Galaxy instance, then Laniakea takes care of automatic deployment of virtual hardware and software components. User gains access with full administrative privileges to private, production grade, fully customized, Galaxy virtual instance, and to underlying virtual machine.

Proper citation: Laniakea (RRID:SCR_018146) Copy   

•   Source: SciCrunch Registry

https://omics.pnl.gov/software/ms-gf

Software that performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.

Proper citation: MS-GF+ (RRID:SCR_015646) Copy   

•   Source: SciCrunch Registry

https://www.google.com/

American multinational technology company that specializes in internet related services and products, which include online advertising technologies, search engine, cloud computing, software, and hardware. Considered one of Big Four technology companies, alongside Amazon, Apple and Facebook.

Proper citation: Google (RRID:SCR_017097) Copy   

•   Source: SciCrunch Registry

http://phenoscape.org/

Project to create a scalable infrastructure that enables linking phenotypes across different fields of biology by the semantic similarity of their descriptions.

Proper citation: Phenoscape (RRID:SCR_003799) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/iontree.html

Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry.

Proper citation: iontree (RRID:SCR_002813) Copy   

•   Source: SciCrunch Registry

http://www.cprofiler.org/

Web tool for discovery and visualization of differences in amino acid composition. Two samples of amino acid sequences serve as input and a bar chart composed of twenty data points is output.

Proper citation: Composition Profiler (RRID:SCR_014630) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/ProP/

Web application which predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase prediction.

Proper citation: ProP Server (RRID:SCR_014936) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/Tools/psa/genewise/

Gene alignment tool from the EBI which predicts gene structure using similar protein sequences. See also the associated GenomeWise tool.

Proper citation: GeneWise (RRID:SCR_015054) Copy   

•   Source: SciCrunch Registry

https://github.com/pybel

Software Python package for parsing, validating, compiling, and converting networks encoded in Biological Expression Language.Package consists of network data container, parser and validator, network database manager, data converter and network visualizer. Computational framework for Biological Expression Language. Used to pars BEL documents, validate their semantics, and facilitate data interchange between common formats and database systems like JSON, CSV, Excel, SQL, CX, and Neo4J.

Proper citation: PyBEL (RRID:SCR_017660) Copy   

•   Source: SciCrunch Registry

http://segway.hoffmanlab.org/

The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. The method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling. Segway uses the Graphical Models Toolkit (GMTK) for efficient DBN inference. The software has extensive documentation and was designed from the outset with external users in mind.

Proper citation: Segway - a way to segment the genome (RRID:SCR_004206) Copy   

•   Source: SciCrunch Registry

http://cudasw.sourceforge.net/

CUDASW++ is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST. In this algorithm, we deeply explore the SIMT (Single Instruction, Multiple Thread) and virtualized SIMD (Single Instruction, Multiple Data) abstractions to achieve fast speed. This algorithm has been fully tested on Tesla C1060, Tesla C2050, GeForce GTX 280 and GTX 295 graphics cards, and has been incorporated to NVIDIA Tesla Bio Workbench. * Operating System: Linux * Programming language: CUDA and C * Other requirements: CUDA SDK and Toolkits 2.0 or higher

Proper citation: CUDASW++ (RRID:SCR_008862) Copy   

•   Source: SciCrunch Registry

http://bioen-compbio.bioen.illinois.edu/FusionHunter/

Software for identifying fusion transcripts using paired-end RNA-seq.

Proper citation: FusionHunter (RRID:SCR_011895) Copy   

•   Source: SciCrunch Registry

https://github.com/oushujun/LTR_FINDER_parallel

Software tool for parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons.

Proper citation: LTR_FINDER_parallel (RRID:SCR_018969) Copy   

•   Source: SciCrunch Registry

https://github.com/gevaertlab/BetaVAEImputation

Software tool as deep learning framework based on variational autoencoder to impute missing values in transcriptome and methylome data analysis.

Proper citation: betaVAEImputation (RRID:SCR_018730) Copy   

•   Source: SciCrunch Registry