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http://users.utu.fi/mijopi/Pripper/
A tool that can be used to predict caspase cleavage sites from human protein sequences.
Proper citation: Pripper (RRID:SCR_007129) Copy
http://deconseq.sourceforge.net/
Software tool to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface. The user can upload FASTA or FASTQ files and select the databases used for contamination screening, including seven human genomes, bacterial genomes, and viral genomes. The user can set the thresholds interactivly and see the results directly using the functionality of the graphical interface. The results can be downloaded in joined or separated files in different formats. The coverage-identity plots provide additional information that can guide the selections of the thresholds using color coded points and connecting lines.
Proper citation: DeconSeq (RRID:SCR_007006) Copy
https://code.google.com/p/peakrots/
Bioinformatics analysis software tool for optimized ChIP-seq peak detection written in R.
Proper citation: peakrots (RRID:SCR_007453) Copy
http://cran.r-project.org/web/packages/evora/
R package for quantifying variation in DNA methylation as a cancer biomarker.
Proper citation: EVORA (RRID:SCR_007329) Copy
http://seurat.r-forge.r-project.org/
Software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data. Visual analytics for the integrated analysis of microarray data.
Proper citation: SEURAT (RRID:SCR_007322) Copy
https://github.com/steinmann/peakzilla
An algorithm to identify transcription factor binding sites from ChIP-seq data.
Proper citation: Peakzilla (RRID:SCR_007471) Copy
Software for identifying haplogroups from low coverage sequence data.
Proper citation: YHap (RRID:SCR_007951) Copy
https://code.google.com/p/ampliconnoise/
A collection of programs for the removal of noise from 454 sequenced PCR amplicons. This project also includes the Perseus algorithm for chimera removal.
Proper citation: AmpliconNoise (RRID:SCR_007814) Copy
Software package that contains a collection of statistical tools for analysing RNA-seq expression data.
Proper citation: MMSEQ (RRID:SCR_008184) Copy
A REST-based web application designed for visualizing deep sequencing data and other genome annotation data.
Proper citation: Anno-J (RRID:SCR_008192) Copy
http://web1.sph.emory.edu/users/hwu30/polyaPeak.html
An R package for ranking ChIP-seq peaks with shape information.
Proper citation: polyaPeak (RRID:SCR_007687) Copy
https://sites.google.com/site/dadadenoiser/
Infers both the sample genotypes and error parameters that produced a metagenome data set.
Proper citation: DADA (RRID:SCR_008205) Copy
http://www.ensembl.org/info/docs/tools/vep/index.html
Data analysis service to predict the functional consequences of known and unknown variants.
Proper citation: Variant Effect Predictor (RRID:SCR_007931) Copy
http://www.bioconductor.org/packages/2.6/bioc/html/DEGseq.html
R package to identify differentially expressed genes from RNA-Seq data.
Proper citation: DEGseq (RRID:SCR_008480) Copy
http://emboss.sourceforge.net/
Software analysis package for molecular biology community. Automatically copes with data in variety of formats and allows transparent retrieval of sequence data from web. Libraries are provided with package. Provides toolkit for creating bioinformatics applications or workflows. Provides set of sequence analysis programs. Provided programs cover areas such as sequence alignment, rapid database searching with sequence patterns, protein motif identification, nucleotide sequence pattern analysis, codon usage analysis for small genomes, rapid identification of sequence patterns in large scale sequence sets, and presentation tools for publication.
Proper citation: EMBOSS (RRID:SCR_008493) Copy
The directing and coordinating authority responsible for public health within the United Nations system. The WHO Regional Office for Europe (WHO/Europe) is one of the six regional offices around the world. It serves the WHO European Region, which comprises 53 countries from the Atlantic to the Pacific oceans. WHO/Europe collaborates with a range of public health stakeholders in the Region and globally, to ensure that coordinated action is taken to develop and implement efficient health policies and to strengthen health systems. WHO/Europe is made up of public health, scientific, and technical experts.
Proper citation: World Health Organization (RRID:SCR_008505) Copy
http://bioinfo-out.curie.fr/projects/vamp/
Software for visualization and Analysis of CGH arrays, transcriptome and other Molecular Profiles.
Proper citation: VAMP (RRID:SCR_008527) Copy
A cloud platform for next-generation sequencing analysis.
Proper citation: Seven Bridges Genomics (RRID:SCR_008308) Copy
http://epicenter.immunbio.mpg.de/services/chromos/
Combines genetic and epigenetic data to facilitate SNP classification, prioritization and prediction of their functional effect.
Proper citation: ChroMoS (RRID:SCR_008320) Copy
https://sites.google.com/site/drivermutationidentification/
Computational tool developed to help identify cancer-associated ''driver'' mutations from ''passenger'' ones in a cancer genome.
Proper citation: DMI (RRID:SCR_008599) Copy
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