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http://www.ch.embnet.org/software/BOX_form.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. This server takes a multiple-alignment file in either GCG''s MSF-format or Clustals ALN-format. Sponsors: This resource was supported by the Swiss EMBnet Node Server. Keywords: Server, Multiple-alignment,, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: BOXSHADE 3.21 (RRID:SCR_007165) Copy
http://202.97.205.78/epidiff/QDMRTutorial.jsp
Software that provides a quantitative approach to quantify methylation difference and identify DMRs from genome-wide methylation profiles by adapting Shannon entropy.
Proper citation: QDMR (RRID:SCR_007162) Copy
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://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://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
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
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
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
A REST-based web application designed for visualizing deep sequencing data and other genome annotation data.
Proper citation: Anno-J (RRID:SCR_008192) 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
Software package that contains a collection of statistical tools for analysing RNA-seq expression data.
Proper citation: MMSEQ (RRID:SCR_008184) 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
http://www.bioconductor.org/packages/release/bioc/html/factDesign.html
Software package that provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection.
Proper citation: factDesign (RRID:SCR_001330) Copy
http://sourceforge.net/projects/ngsrich/
Software for target enrichment performance for next-generation sequencing.
Proper citation: NGSrich (RRID:SCR_001333) Copy
http://www.bioconductor.org/packages/release/bioc/html/pickgene.html
Software for adaptive Gene Picking for Microarray Expression Data Analysis.
Proper citation: pickgene (RRID:SCR_001331) Copy
https://www.bioconductor.org/packages//2.10/bioc/html/oneChannelGUI.html
Software library that provides a graphical interface for microarray gene and exon level analysis as well as miRNA/mRNA-seq data analysis. The package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code.
Proper citation: oneChannelGUI (RRID:SCR_001325) Copy
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