:: DESCRIPTION
VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules.
Wala J, Zhang CZ, Meyerson M, Beroukhim R.
Bioinformatics. 2016 Feb 26. pii: btw111.
:: DESCRIPTION
SynthEx is a comprehensive suite of tools for CNA detection and tumor heterogeneity profiling. It is tailored to cater for the multiple characteristics of different next generation sequencing technologies.
::DEVELOPER
Chen Group at U Chicago
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Silva GO, Siegel MB, Mose LE, Parker JS, Sun W, Perou CM, Chen M.
SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling.
Genome Biol. 2017 Apr 8;18(1):66. doi: 10.1186/s13059-017-1193-3. PMID: 28390427; PMCID: PMC5385048.
:: DESCRIPTION
The metaBIT pipeline proposes tools for visualising microbial profiles (barplots, heatmaps) and performing a range of statistical analyses (diversity indices, hierarchical clustering and principal coordinate analysis). It uses as input fastq files containing trimmed reads from shotgun high through-put sequencing.
::DEVELOPER
The Centre for Anthropobiology and Genomics of Toulouse
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Louvel G, Der Sarkissian C, Hanghoj K, Orlando L.
metaBIT, an integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data.
Mol Ecol Resour. 2016 Nov;16(6):1415-1427. doi: 10.1111/1755-0998.12546. Epub 2016 Jun 22. PMID: 27238636.
:: DESCRIPTION
X2K (Expression2Kinases) is a method to identify upstream regulators likely responsible for observed patterns in genome-wide gene expression. By integrating ChIP-seq/chip and position-weight-matrices (PWMs) data, protein-protein interactions, and kinase-substrate phosphorylation reactions, X2K can better identify regulatory mechanisms upstream of genome-wide differences in gene expression. X2K first infers the most likely transcription factors that regulate the differences in gene expression, then use protein-protein interactions to connect the identified transcription factors using additional proteins for building transcriptional regulatory subnetworks centered on these factors, and finally use kinase-substrate protein phosphorylation reactions, to identify and rank candidate protein-kinases that most likely regulate the formation of the identified transcriptional complexes.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Chen EY, Xu H, Gordonov S, Lim MP, Perkins MH, Ma’ayan A.
Expression2Kinases: mRNA Profiling Linked to Multiple Upstream Regulatory Layers.
Bioinformatics. (2012) 28 (1): 105-111
:: DESCRIPTION
NOVA is a program designed to analysis complexome profiling data. A graphical user interface (GUI) provides various visualization tools, such as heat maps and 2D plots. nova gui Several hierarchical clustering algorithms (e.g., single linkage, average linkage, Wards linkage), different distance measures (e.g., Euclidean distance, Manhattan distance, Pearson distance), and various normalization techniques are implemented. Many additional functions like zooming, searching for proteins, image export, and automatic file format recognition support intuitive handling for biologists.
::DEVELOPER
Molecular Bioinformatics MolBI
:: SCREENSHOTS
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
NOVA: a software to analyze complexome profiling data.
Giese H, Ackermann J, Heide H, Bleier L, Dröse S, Wittig I, Brandt U, Koch I.
Bioinformatics. 2014 Oct 9. pii: btu623
Cell Metabolism, 16:538–549, 2012.
:: DESCRIPTION
GeneNetWeaver (GNW) is an open-source tool for in silico benchmark generation and performance profiling of network inference methods.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Schaffter, T. et al. (2011).
GeneNetWeaver: In silico benchmark generation and performance profiling of network inference methods.
Bioinformatics, 27(16):2263-70
:: DESCRIPTION
The mOTUs profiler is a computational tool that estimates relative abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Microbial abundance, activity and population genomic profiling with mOTUs2
Alessio Milanese, et al.
Nature Communications 10, Article number: 1014 (2019): https://doi.org/10.1038/s41467-019-08844-4
:: DESCRIPTION
MiRCat is a revolutionary new way of sharing and analysing sequencing data for small RNA.
::DEVELOPER
Victor Chang Cardiac Research Institute
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Nucleic Acids Res. 2013 Aug 1;41(15):e147. doi: 10.1093/nar/gkt485. Epub 2013 Jun 17.
miRspring: a compact standalone research tool for analyzing miRNA-seq data.
Humphreys DT, Suter CM.
:: DESCRIPTION
GEPIS (Gene Expression Profiling in silico), is a bioinformatics tool that integrates EST and tissue source information to compute gene expression patterns in a large panel of normal and tumor samples.
::DEVELOPER
UCSF CGL -Genentech Collaboration
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Yan Zhang, David A. Eberhard, Gretchen D. Frantz, Patrick Dowd, Thomas D. Wu, Yan Zhou, Colin Watanabe, Shiuh-Ming Luoh, Paul Polakis, Kenneth J. Hillan, William I. Wood and Zemin Zhang
GEPIS-quantitative gene expression profiling in normal and cancer tissues
Bioinformatics, Oct. 12 2004, Vol. 20, No. 15, pp2390-2398
:: DESCRIPTION
ProfCom is a web-based tool for the functional interpretation of a gene list that was identified to be related by experiments.
::DEVELOPER
Willkommen am Lehrstuhl für Genomorientierte Bioinformatik der TU München.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W347-51. doi: 10.1093/nar/gkn239. Epub 2008 May 6.
ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data.
Antonov AV, Schmidt T, Wang Y, Mewes HW.
