:: DESCRIPTION
GeneViewer is very simple program for visualising the locations of various genomic features (SNPs, exons etc.)along a sequence. The user enters start and stop coordinates of the region they’re interested in, followed by any number of files. Each file must contain 2 columns of data (region start & stop) with any number of rows
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
EFFECT is an algorithmic framework for automated detection of functional signals in biological sequences.
::DEVELOPER
Computational Biology lab, George Mason University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kamath U, De Jong K, Shehu A.
Effective automated feature construction and selection for classification of biological sequences.
PLoS One. 2014 Jul 17;9(7):e99982. doi: 10.1371/journal.pone.0099982. PMID: 25033270; PMCID: PMC4102475.
:: DESCRIPTION
repDNA (Representations of DNAs) is a Python package for generating the widely used features reflecting the physicochemical properties and sequence-order effects of DNAs and nucleotides.
::DEVELOPER
Liu Lab, Harbin Institute of Technology Shenzhen Graduate School.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects.
Liu B, Liu F, Fang L, Wang X, Chou KC.
Bioinformatics. 2014 Dec 10. pii: btu820.
:: DESCRIPTION
Spial (Specificity in alignments) is a web-server that takes a pair of multiple sequence alignments as input and produces an output that highlights positions which are conserved in both alignments (the consensus), and positions which are specific to either alignment.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Bioinformatics. 2010 Nov 15;26(22):2906-7. doi: 10.1093/bioinformatics/btq552. Epub 2010 Sep 29.
Spial: analysis of subtype-specific features in multiple sequence alignments of proteins.
Wuster A1, Venkatakrishnan AJ, Schertler GF, Babu MM.
:: DESCRIPTION
ProFET: Protein Feature Engineering Toolkit for Machine Learning
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
ProFET: Feature engineering captures high-level protein functions.
Ofer D, Linial M.
Bioinformatics. 2015 Jun 30. pii: btv345.
:: DESCRIPTION
Fizzy is a feature subset selection tool that uses FEAST in the background to run feature selection on biological data formats.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Fizzy: feature subset selection for metagenomics.
Ditzler G, Morrison JC, Lan Y, Rosen GL.
BMC Bioinformatics. 2015 Nov 4;16:358. doi: 10.1186/s12859-015-0793-8.
:: DESCRIPTION
Igloo-Plot is a tool for efficient visualization of multidimensional datasets.
Web-Igloo visualizes multivariate data in a 2D chart of multiple quantitative variables represented as anchors on a semicircle.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kuntal BK, Ghosh TS, Mande SS.
Igloo-Plot: a tool for visualization of multidimensional datasets.
Genomics. 2014 Jan;103(1):11-20. doi: 10.1016/j.ygeno.2014.01.004. Epub 2014 Jan 17. PMID: 24444495.
Kuntal BK, Mande SS.
Web-igloo: a web based platform for multivariate data visualization.
Bioinformatics. 2017 Feb 15;33(4):615-617. doi: 10.1093/bioinformatics/btw669. PMID: 27797774.
:: DESCRIPTION
Alfred is an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner. Alfred supports read counting, feature annotation and haplotype-resolved consensus computation using multiple sequence alignments
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Rausch T, Hsi-Yang Fritz M, Korbel JO, Benes V.
Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing.
Bioinformatics. 2019 Jul 15;35(14):2489-2491. doi: 10.1093/bioinformatics/bty1007. PMID: 30520945; PMCID: PMC6612896.
:: DESCRIPTION
ZMap is a genome browser written in C with the aim of providing fast access to high volume data. Data may be requested from a variety of disparate sources in parallel and cached locally allowing new tracks to be loaded or the view of current data adjusted without delay. Multiple views of the data may be presented and tracks configured for different levels of detail.
::DEVELOPER
the Annotools team at the Sanger Institute zmap@sanger.ac.uk
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
mRMRe contains a set of function to compute mutual information matrices from continuous, categorical and survival variables. It also contains function to perform feature selection with minimum Redundancy, Maximum Relevance (mRMR) and a new ensemble mRMR technique.
::DEVELOPER
Princess Margaret Bioinformatics and Computational Genomics Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2013 Sep 15;29(18):2365-8. doi: 10.1093/bioinformatics/btt383. Epub 2013 Jul 3.
mRMRe: an R package for parallelized mRMR ensemble feature selection.
De Jay N, Papillon-Cavanagh S, Olsen C, El-Hachem N, Bontempi G, Haibe-Kains B.
