Tag: Difference

quandico 1.14 – Quantitative Analysis of differences in Copy Numbers

quandico 1.14

:: DESCRIPTION

The tool quandico applies statistical methods to detect copy number variations (CNV) in a sample by comparing the read counts from next generation sequencing (NGS) performed after PCR-enrichment of regions of interest, typically a set of genes with known or expected relevance for the sample, e.g. genes that play a role in cancer. Counts from a normal control (ideally matched normal from the same individual, e.g. healthy tissue) are required.

::DEVELOPER

Frank Reinecke

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
  • Perl

:: DOWNLOAD

 quandico

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2015 Jan 28;16(1):17.
Quantitative analysis of differences in copy numbers using read depth obtained from PCR-enriched samples and controls.
Reinecke F, Satya R, DiCarlo J.

GENE-counter 0.4.4 – Analysis of RNA-Seq data for Gene Expression Differences

GENE-counter 0.4.4

:: DESCRIPTION

GENE-counter is a computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression of eukaryotes, prokaryotes, as well as organisms with no available genome reference sequence.

::DEVELOPER

the Chang Lab, Oregon State University,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Perl

:: DOWNLOAD

GENE-counter

:: MORE INFORMATION

Citation

PLoS One. 2011;6(10):e25279. doi: 10.1371/journal.pone.0025279. Epub 2011 Oct 6.
GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences.
Cumbie JS, Kimbrel JA, Di Y, Schafer DW, Wilhelm LJ, Fox SE, Sullivan CM, Curzon AD, Carrington JC, Mockler TC, Chang J

rddChecker – software for Detecting RNA-DNA Differences

rddChecker

:: DESCRIPTION

rddChecker is a program for determining sites of RNA-DNA differences (RDDs) and candidate RNA editing sites from RNA-seq data.

::DEVELOPER

Center for Computational Biology , Johns Hopkins University School of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  rddChecker

:: MORE INFORMATION

Citation

Florea, L. and S.L. Salzberg (2011).
Accurate detection of RNA-DNA differences in RNA-seq data with rddChecker.
Cold Spring Harbor Laboratory Meeting – Genome Informatics, Cold Spring Harbor, NY

Composition Profiler 1.1 – Discovery of Amino Acid Composition Differences

Composition Profiler 1.1

:: DESCRIPTION

Composition Profiler is a web-based tool that automates detection of enrichment or depletion patterns of individual amino acids or groups of amino acids classified by several physico-chemical and structural properties.

Composition Profiler Online

:: SCREENSHOTS

N/A

::DEVELOPER

Vladimir Vacic and Stefano Lonardi (University of California, Riverside), and Vladimir N. Uversky and A. Keith Dunker (Indiana University School of Medicine, Indianapolis).

:: REQUIREMENTS

:: DOWNLOAD

 Composition Profiler

:: MORE INFORMATION

Citation:

Vacic V., Uversky V.N., Dunker A.K., and Lonardi S.
“Composition Profiler: A tool for discovery and visualization of amino acid composition differences“.
BMC Bioinformatics. 8:211. (2007