Tag: Analyzer

rSeq 0.2.1 – RNA-Seq Analyzer

rSeq 0.2.1

:: DESCRIPTION

rSeq is a set of tools for RNA-Seq data analysis. It consists of programs that deal with many aspects of RNA-Seq data analysis, such as reference sequence generation, sequence mapping, gene and isoform expressions (RPKMs) computation, etc. There are also many other features that will be gradually added into rSeq in the future.

::DEVELOPER

Hui Jiang.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

  rSeq

:: MORE INFORMATION

Reference

Jiang, H., Wong, W.H. (2009) Statistical Inferences for Isoform Expression in RNA-Seq, Bioinformatics, 25(8), 1026–1032. [online][preprint]

Salzman, J., Jiang, H., Wong, W. H. (2011) Statistical Modeling of RNA-Seq Data, Statistical Science, 26 (1): 62-83. [online][arxiv]

AnCorr – Genome Track Analyzer

AnCorr

:: DESCRIPTION

AnCorr is the set of tools for genome-wide study of genomic features and their correlations.The tools is designed to compare genome tracks by robust method with their attribution relative to DNA strands.

::DEVELOPER

AnCorr team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Genome-wide study of correlations between genomic features and their relationship with the regulation of gene expression.
Kravatsky YV, Chechetkin VR, Tchurikov NA, Kravatskaya GI.
DNA Res. 2015 Feb;22(1):109-19. doi: 10.1093/dnares/dsu044.

mirnaTA 1.2.3 – miRNA Temporal Analyzer

mirnaTA 1.2.3

:: DESCRIPTION

mirnaTA is a bioinformatics tool which can be used to identify differentially expressed miRNAs in temporal studies.

::DEVELOPER

mirnaTA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • R

:: DOWNLOAD

 mirnaTA

:: MORE INFORMATION

Citation:

miRNA Temporal Analyzer (mirnaTA): a bioinformatics tool for identifying differentially expressed microRNAs in temporal studies using normal quantile transformation.
Cer RZ, Herrera-Galeano JE, Anderson JJ, Bishop-Lilly KA, Mokashi VP.
Gigascience. 2014 Oct 13;3:20. doi: 10.1186/2047-217X-3-20.

PROVEAN 1.1.5 – Protein Variation Effect Analyzer

PROVEAN 1.1.5

:: DESCRIPTION

PROVEAN is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.

::DEVELOPER

PROVEAN Team, J. Craig Venter Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PROVEAN

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Apr 6. pii: btv195.
PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels.
Choi Y, P Chan A

PLoS One. 2012;7(10):e46688. doi: 10.1371/journal.pone.0046688. Epub 2012 Oct 8.
Predicting the functional effect of amino acid substitutions and indels.
Choi Y, Sims GE, Murphy S, Miller JR, Chan AP.

C2Analyzer – Cotarget-Cofunction Analyzer

C2Analyzer

:: DESCRIPTION

The C2Analyzer: Co-target-Co-function Analyzer, is a Perl-based, versatile and user-friendly web tool with online instructions. Based on the hypergeometric analysis, this novel tool can determine whether given pairs of miRNAs are co-functionally enriched.

::DEVELOPER

C2Analyzer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

C2Analyzer: Co-target-co-function analyzer.
Aftabuddin M, Mal C, Deb A, Kundu S.
Genomics Proteomics Bioinformatics. 2014 Jun;12(3):133-6. doi: 10.1016/j.gpb.2014.03.003.

ADZE 1.0 – Allelic Diversity Analyzer

ADZE 1.0

:: DESCRIPTION

ADZE is a program that implements the rarefaction method for analyzing allelic diversity across populations while correcting for sample size differences. Using individual multilocus genotype data on genetic polymorphisms, ADZE computes estimates of allelic richness, private allelic richness, and private allelic richness for combinations of populations.

::DEVELOPER

Rosenberg lab at Stanford University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 ADZE

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Nov 1;24(21):2498-504. doi: 10.1093/bioinformatics/btn478. Epub 2008 Sep 8.
ADZE: a rarefaction approach for counting alleles private to combinations of populations.
Szpiech ZA, Jakobsson M, Rosenberg NA.

pFlexAna 0.1.1 – Protein Flexibility Analyzer

pFlexAna 0.1.1

:: DESCRIPTION

The pFlexAna  detects and displays conformational changes in remotely related proteins, without relying on sequence homology

::DEVELOPER

M2AP Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • C++ Compiler

:: DOWNLOAD

 pFlexAna

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W246-51. doi: 10.1093/nar/gkn259.
pFlexAna: detecting conformational changes in remotely related proteins.
Nigham A, Tucker-Kellogg L, Mihalek I, Verma C, Hsu D.

SWAN 0.3.0 – Statistical Structural Variation ANalyzer

SWAN 0.3.0

:: DESCRIPTION

SWAN is the first to introduce a statistically verifiable heterogeneity SV model to the community. As in SWAN, the genetic material sampled is no longer viewed as a homogenous mutant or reference sample but explicitly modeled as a mixture of both mutant and reference sequences with their fractions estimable.

::DEVELOPER

Ji Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • R

:: DOWNLOAD

SWAN

:: MORE INFORMATION

Citation

A genome-wide approach for detecting novel insertion-deletion variants of mid-range size.
LC Xia, S Sakshuwong, E Hopmans, J Bell, S Grimes, D Siegmund, H Ji, Nancy Zhang.
Nucleic Acids Research 44 (15), e126 (2016)

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