ABCreg 0.1.0 – Automating Approximate Bayesian Computation by Local Linear Regression

ABCreg 0.1.0

:: DESCRIPTION

ABCreg is a tool for performing statistical inference via approximate Bayesian computation, or ABC.

::DEVELOPER

Thornton Lab at UC Irvine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 ABCreg

:: MORE INFORMATION

Citation

BMC Genet. 2009 Jul 7;10:35. doi: 10.1186/1471-2156-10-35.
Automating approximate Bayesian computation by local linear regression.
Thornton KR

CGDSR 1.3.0 / CGDS Toolbox 1.07 – Accessing the MSKCC Cancer Genomics Data Server (CGDS)

CGDSR 1.3.0 / CGDS Toolbox 1.07

:: DESCRIPTION

The CGDS-R package provides a basic set of R functions for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).

CGDS Toolbox provides direct access to cancer genomics data from within the MATLAB environment.

::DEVELOPER

CGDS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • MatLab / R package 

:: DOWNLOAD

   CGDSR/ CGDS Toolbox

:: MORE INFORMATION

inTB – Platform for Molecular and Clinical Epidemiological Analysis of Tuberculosis

inTB

:: DESCRIPTION

inTB is a web-based system for storage and analysis of clinical, socio-demographic and molecular typing data.

::DEVELOPER

inTB team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 inTB

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Aug 30;14:264. doi: 10.1186/1471-2105-14-264.
inTB – a data integration platform for molecular and clinical epidemiological analysis of tuberculosis.
Soares P1, Alves RJ, Abecasis AB, Penha-Gonçalves C, Gomes MG, Pereira-Leal JB.

TEQC 4.12.0 – Quality Assessment of Target Enrichment Experiments

TEQC 4.12.0

:: DESCRIPTION

TEQC is an R/Bioconductor package for quality assessment of target enrichment experiments.

::DEVELOPER

Bioinformatics Core @ CRG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • R package
  • BioConductor

:: DOWNLOAD

 TEQC

:: MORE INFORMATION

Citation

Bioinformatics. 2011 May 1;27(9):1316-7. doi: 10.1093/bioinformatics/btr122.
TEQC: an R package for quality control in target capture experiments.
Hummel M, Bonnin S, Lowy E, Roma G.

SR4GN 1.0 – Species Recognition software tool for Gene Normalization

SR4GN 1.0

:: DESCRIPTION

SR4GN is a species recognition software tool for gene normalization.

::DEVELOPER

Zhiyong Lu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows
  • Perl

:: DOWNLOAD

 SR4GN

:: MORE INFORMATION

Citation

PLoS One. 2012;7(6):e38460. doi: 10.1371/journal.pone.0038460. Epub 2012 Jun 5.
SR4GN: a species recognition software tool for gene normalization.
Wei CH, Kao HY, Lu Z.

PubTator – Text Mining tool for Assisting Biocuration

PubTator

:: DESCRIPTION

PubTator is a Web-based tool for accelerating manual literature curation (e.g. annotating biological entities and their relationships) through the use of advanced text-mining techniques. As an all-in-one system, PubTator provides one-stop service for annotating PubMed citations.

::DEVELOPER

Zhiyong Lu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Wei CH, Kao HY, Lu Z.,
PubTator: a Web-based text mining tool for assisting Biocuration,
Nucleic acids research, 2013, 41 (W1): W518-W522. doi: 10.1093/nar/gkt44

tmVar 2.0 – Text Mining approach for Extracting Sequence Variants in Biomedical Literature

tmVar 2.0

:: DESCRIPTION

tmVar is a text-mining approach based on conditional random field (CRF) for extracting a wide range of sequence variants in both protein and gene levels according to a standard sequence variants nomenclature developed by the human genome variation society (HGVS).

::DEVELOPER

Zhiyong Lu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 tmVar

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jun 1;29(11):1433-9. doi: 10.1093/bioinformatics/btt156. Epub 2013 Apr 5.
tmVar: a text mining approach for extracting sequence variants in biomedical literature.
Wei CH, Harris BR, Kao HY, Lu Z.

References On Tap – Your reference manager for iOS

References On Tap

:: DESCRIPTION

References On Tap (previously PubMed On Tap) is an application for your iPhone, iPod Touch, and iPad that lets you search PubMed and PubMed Central while on the go.

::DEVELOPER

References On Tap team

:: SCREENSHOTS

:: REQUIREMENTS

  • iPad/iPhone

:: DOWNLOAD

 PubMed On Tap

:: MORE INFORMATION

GEOquery 2.58.0 – Get data from NCBI Gene Expression Omnibus (GEO)

GEOquery 2.58.0

:: DESCRIPTION

GEOquery effectively establishes a bridge between GEO and BioConductor. Easy access to GEO data from BioConductor will likely lead to new analyses of GEO data using novel and rigorous statistical and bioinformatic tools.

::DEVELOPER

Sean Davis @NCI

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 GEOquery

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Jul 15;23(14):1846-7.
GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor.
Davis S, Meltzer PS.

dendsort 0.2 – Optimize Ordering of Nodes in a Dendrogram

dendsort 0.2

:: DESCRIPTION

dendsort includes functions to optimize ordering of nodes in a dendrogram, without affecting the meaning of the dengrogram. A dengrogram can be sorted based on the average distance of subtrees, or based on the smallest distance value. These sorting methods improve readability and interpretability of tree structure, especially for tasks such as comparison of different disntance measures or linkage types and identification of tight clusters and outliers. As a result, it also introduces more meaningful reordering for a coupled heatmap visualization.

::DEVELOPER

Bioinformatics Research Group, Belgium

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • R package

:: DOWNLOAD

 dendsort

:: MORE INFORMATION