ESTprep 3.1.4 – Preprocessing cDNA Sequence Reads

ESTprep 3.1.4

:: DESCRIPTION

ESTprep is a program that performs the preprocessing for cDNA reads. It is a part of ESTprep Suite which contains other utilities for producing different levels of output, including HTML formatted file. The program detects all the characterstics found within a sequence viz. restriction site, cloning vector, polyA tail, library tag, polyA signal. It also predicts whether the sequence should be used for further processing or should be rejected. If accepted the region within the sequence which is high quality is also identified.

::DEVELOPER

Coordinated Laboratory for Computational Genomics (CLCG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Compiler

:: DOWNLOAD

ESTprep

:: MORE INFORMATION

Citation

Bioinformatics. 2003 Jul 22;19(11):1318-24.
ESTprep: preprocessing cDNA sequence reads.
Scheetz TE1, Trivedi N, Roberts CA, Kucaba T, Berger B, Robinson NL, Birkett CL, Gavin AJ, O’Leary B, Braun TA, Bonaldo MF, Robinson JP, Sheffield VC, Soares MB, Casavant TL.

illumina 1.0.6 – Preprocessing Illumina Whole Genome Expression BeadChips

illumina 1.0.6

:: DESCRIPTION

illumina is an R Library for preprocessing Illumina Whole Genome Expression BeadChips.

::DEVELOPER

WEHI Bioinformatics

:: SCREENSHOTS

N/a

:: REQUIREMENTS

Windows / Linux / MacOsX
R package

:: DOWNLOAD

illumina

:: MORE INFORMATION

Citation

Shi, W., Banerjee, A., Ritchie, M. E., Gerondakis, S., and Smyth, G. K.
Illumina WG-6 BeadChip strips should be normalized separately.
BMC Bioinformatics, 2009 Nov 11;10(1):372. [Epub ahead of print], PMID: 19903361

MEAP 2.0.2 – Multiple Exon Array Preprocessing

MEAP 2.0.2

:: DESCRIPTION

MEAP is an R package for large-scale exon array data analysis.It includes a novel algorithm (PM-BayesBG) to estimate sequence-based backgrounds that allows more reliable expression estimation than the existing background correction methods. MEAP also contains algorithms for generating robust expression estimates at exon, alternatively spliced variant and gene levels that facilitates the quantitative analysis of alternative spliced variants in the whole transcriptome.

::DEVELOPER

Hautaniemi Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
R Package

:: DOWNLOAD

MEAP

:: MORE INFORMATION

Citation

Chen P, Lepikhova T, Hu YZ, Monni O and Hautaniemi S.
Comprehensive Exon Array Data Processing Method for Quantitative Analysis of Alternative Spliced Variants.
Nucleic Acids Research. 2011 Oct;39(18):e123. Epub 2011 Jul 10.

fRMA 1.39.0 / frmaTools 1.39.0 – Single Microarray Preprocessing and Analysis

fRMA 1.39.0 / frmaTools 1.39.0

:: DESCRIPTION

fRMA (Frozen robust multiarray analysis) is a single-array preprocessing algorithm that retains the advantages of multiarray algorithms and removes certain batch effects by downweighting probes that have high between-batch residual variance.

frmaTools: Extension and customization of the frma package.

::DEVELOPER

Matthew N. McCall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / MacOsX / Linux
R package
Bioconductor

:: DOWNLOAD

fRMA / frmaTools

:: MORE INFORMATION

Citation

Thawing Frozen Robust Multi-array Analysis (fRMA).
McCall MN, Irizarry RA.
BMC Bioinformatics. 2011 Sep 16;12:369. doi: 10.1186/1471-2105-12-369.

affyParaEBI 1.0.0 – Preprocessing of Microarray Experiments

affyParaEBI 1.0.0

:: DESCRIPTION

The affyParaEBI is an R based pipeline for parallel pre-processing of Affymetrix TM chips. The pipeline starts from a directory containing raw CEL files files and produces Bioconductor R objects containing gene expression measurements suitable for further analysis.

::DEVELOPER

EBI.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R package
Bioconductor

:: DOWNLOAD

affyParaEBI

:: MORE INFORMATION