:: DESCRIPTION
BroadPeak is an algorithm for the identification of broad peaks from diffuse ChIP-seq datasets.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Feb 15;29(4):492-3. doi: 10.1093/bioinformatics/bts722. Epub 2013 Jan 7.
BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets.
Wang J, Lunyak VV, Jordan IK.
:: DESCRIPTION
SECISaln predicts eukaryotic SECIS elements in a sequence and aligns them against a precompiled database of eukaryotic SECIS elements.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
No. Only web service.
:: MORE INFORMATION
Citation
Bioinformatics. 2009 Mar 1;25(5):674-5. Epub 2009 Jan 29.
SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements.
Chapple CE, Guigó R, Krol A.
:: DESCRIPTION
DatasetAssess is a tool to estimate error rates in high-throughput protein interaction datasets and other functional genomic data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Gilchrist, M.A., Salter, L.A., Wagner, A. (2004)
A statistical framework for combining and interpreting proteomic datasets.
Bioinformatics 20, 689-700
:: DESCRIPTION
Chimerascan is a software for detecting gene fusions in paired-end RNA sequencing (RNA-Seq) datasets.
::DEVELOPER
The Michigan Center for Translational Pathology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2011 Oct 15;27(20):2903-4. Epub 2011 Aug 11.
ChimeraScan: a tool for identifying chimeric transcription in sequencing data.
Iyer MK, Chinnaiyan AM, Maher CA.
:: DESCRIPTION
DiffSplice is a novel tool for discovering and quantitating alternative splicing variants present in an RNA-seq dataset, without relying on annotated transcriptome or pre-determined splice pattern. For two groups of samples, DiffSplice further utilizes a non-parametric permutation test to identify significant differences in expression at both gene level and transcription level. DiffSplice takes as input the SAM files that supply the alignment of the RNA-seq reads on the reference genome, obtained from an RNA-seq aligner like MapSplice. The results of DiffSplice are summarized as a decomposition of the genome and can be visualized using the UCSC genome browser.
::DEVELOPER
Bioinformatics Lab @CS.UKy.edu
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Nucleic Acids Res. 2013 Jan;41(2):e39. doi: 10.1093/nar/gks1026. Epub 2012 Nov 15.
DiffSplice: the genome-wide detection of differential splicing events with RNA-seq.
Hu Y, Huang Y, Du Y, Orellana CF, Singh D, Johnson AR, Monroy A, Kuan PF, Hammond SM, Makowski L, Randell SH, Chiang DY, Hayes DN, Jones C, Liu Y, Prins JF, Liu J.
:: DESCRIPTION
Myrna is a cloud computing tool for calculating differential gene expression in large RNA-seq datasets. Myrna uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization, and statistical testing. These tools are combined in an automatic, parallel pipeline that runs in the cloud (Elastic MapReduce in this case) on a local Hadoop cluster, or on a single computer, exploiting multiple computers and CPUs wherever possible.
::DEVELOPER
Ben Langmead, Kasper Hansen, and Jeffrey Leek
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Biol. 2010;11(8):R83. doi: 10.1186/gb-2010-11-8-r83. Epub 2010 Aug 11.
Cloud-scale RNA-sequencing differential expression analysis with Myrna.
Langmead B, Hansen KD, Leek JT.
:: DESCRIPTION
Frida (FRamework for Image Dataset Analysis) is image analysis software. Frida was developed by the Johns Hopkins University Tissue Microarray Core Facility. Frida is open source and written in 100% Java. Frida makes use of functionality from the NIH’s ImageJ application.
::DEVELOPER
JHU Tissue MicroArray Core Facility
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Cornish T, Morgan J, Gurel B, and De Marzo AM.
FrIDA: An open source framework for image dataset analysis.
Arch. Pathol. Lab. Med. 132:856 (2008). Originally presented at Advancing Practice, Instruction and Innovation Through Informatics: Pittsburgh, PA, 2007.
:: DESCRIPTION
SEDA is an open source application for processing FASTA files containing DNA and protein sequences.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Lopez-Fernandez H, Duque P, Vazquez N, Fdez-Riverola F, Reboiro-Jato M, Vieira CP, Vieira J.
SEDA: a Desktop Tool Suite for FASTA Files Processing.
IEEE/ACM Trans Comput Biol Bioinform. 2020 Nov 25;PP. doi: 10.1109/TCBB.2020.3040383. Epub ahead of print. PMID: 33237866.
:: DESCRIPTION
HAPGEN simulates case control datasets at SNP markers. The new version can now simulate multiple disease SNPs on a single chromosome, on the assumption that each disease SNP acts independently and are in Hardy-Weinberg equilibrium. We also supply a R package that can simulate interaction between the disease SNPs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Chris C. A. Spencer, Zhan Su, Peter Donnelly, Jonathan Marchini (2009)
Designing Genome-Wide Association Studies: Sample Size, Power, Imputation, and the Choice of Genotyping Chip.
PLoS Genet 5(5).
:: DESCRIPTION
ccPDB is designed to provide service to scientific community working in the field of function or structure annoation of proteins. This database of datasets is based on Protein Data Bank (PDB), where all datasets were derived from PDB. ccPDB have four modules; i) compilation of datasets, ii) creation of datasets, iii) web services and iv) Important links.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
ccPDB 2.0: an updated version of datasets created and compiled from Protein Data Bank.
Agrawal P, Patiyal S, Kumar R, Kumar V, Singh H, Raghav PK, Raghava GPS.
Database (Oxford). 2019 Jan 1;2019. doi: 10.1093/database/bay142.
ccPDB: compilation and creation of data sets from Protein Data Bank.
Singh H, Chauhan JS, Gromiha MM; Open Source Drug Discovery Consortium, Raghava GP.
Nucleic Acids Res. 2012 Jan;40(Database issue):D486-9. doi: 10.1093/nar/gkr1150.