GeneNetWeaver 3.1.3 Beta – in silico benchmark Generation and performance profiling of Network Inference Methods

GeneNetWeaver 3.1.3 Beta

:: DESCRIPTION

GeneNetWeaver (GNW) is an open-source tool for in silico benchmark generation and performance profiling of network inference methods.

::DEVELOPER

GeneNetWeaver team

:: SCREENSHOTS

GeneNetWeaver

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 GeneNetWeaver

:: 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

mOTUs 2.5.1 – Tool for Marker Gene-based OTU (mOTU) Profiling

mOTUs 2.5.1

:: 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

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

mOTUs

:: 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

X2K 1.6.1207 – mRNA Profiling Linked to Multiple Upstream Regulatory Layers

X2K 1.6.1207

:: 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

Ma’ayan Laboratory

:: SCREENSHOTS

X2K

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java 

:: DOWNLOAD

 X2K

:: 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

VariantBam 1.2.1 – Filtering and Profiling of Next-generational Sequencing data using Region-specific Rules

VariantBam 1.2.1

:: DESCRIPTION

VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files.

::DEVELOPER

VariantBam team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 VariantBam

:: 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.

LobSTR 4.0.0 – Profiling STRs in Personal Genomes

LobSTR 4.0.0

:: DESCRIPTION

lobSTR is a tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data.

::DEVELOPER

Melissa Gymrek

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 LobSTR

:: MORE INFORMATION

Citation

lobSTR: A short tandem repeat profiler for personal genomes.
Gymrek M, Golan D, Rosset S, Erlich Y.
Genome Res. 2012 Jun;22(6):1154-62. doi: 10.1101/gr.135780.111.

ASSIGN 1.6.0 – Adaptive Profiling of Genomic Signatures

ASSIGN 1.6.0

:: DESCRIPTION

ASSIGN (Adaptive Signature Selection and InteGratioN) is a computational tool to evaluate the pathway deregulation/activation status in individual patient samples.

::DEVELOPER

Ying Shen <yshen3 at bu.edu>, Andrea H. Bild, and W. Evan Johnson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

ASSIGN

:: MORE INFORMATION

Citation

ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways.
Shen Y, Rahman M, Piccolo SR, Gusenleitner D, El-Chaar NN, Cheng L, Monti S, Bild AH, Johnson WE.
Bioinformatics. 2015 Jun 1;31(11):1745-53. doi: 10.1093/bioinformatics/btv031.

NOVA 0.5.7 – Visualization and Analysis of Complexome Profiling data

NOVA 0.5.7

:: 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

NOVA

::REQUIREMENTS

  • Windows

:: DOWNLOAD

 NOVA 

:: 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.

metaMix 0.2 – Bayesian Mixture Analysis for Metagenomic Community Profiling

metaMix 0.2

:: DESCRIPTION

metaMix is a Bayesian mixture model framework for resolving complex metagenomic mixtures.

::DEVELOPER

Sofia Morfopoulou <sofia.morfopoulou.10 at ucl.ac.uk>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • R

:: DOWNLOAD

 metaMix

:: MORE INFORMATION

Citation

Bioinformatics. 2015 May 21. pii: btv317.
Bayesian mixture analysis for metagenomic community profiling.
Morfopoulou S, Plagnol V

IntegrationMap / IntegrationSeq – Integration Site Mapping and Profiling / Sequence Trimming and Processing Tool

IntegrationMap / IntegrationSeq

:: DESCRIPTION

IntegrationMap can be used to determine and profile integration sites of viruses or viral vectors on a chromosomal and genomic level.

IntegrationSeq can be used to prepare raw files from an genetic analyzer for mapping to the human genome.

::DEVELOPER

HUSAR Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Methods Inf Med. 2007;46(5):542-7.
New bioinformatic strategies to rapidly characterize retroviral integration sites of gene therapy vectors.
Giordano FA1, Hotz-Wagenblatt A, Lauterborn D, Appelt JU, Fellenberg K, Nagy KZ, Zeller WJ, Suhai S, Fruehauf S, Laufs S.

RandA 1.1.4 – ncRNA Profiling

RandA 1.1.4

:: DESCRIPTION

RandA (ncRNA Read-and-Analyze) allows to analyze all known non-coding RNAs in a cell.

::DEVELOPER

Team Shomron

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • R
  • Java

:: DOWNLOAD

 RandA

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 Jun;40(11):e86. doi: 10.1093/nar/gks228. Epub 2012 Mar 9.
Novel insight into the non-coding repertoire through deep sequencing analysis.
Isakov O1, Ronen R, Kovarsky J, Gabay A, Gan I, Modai S, Shomron N.