MergeMaid 2.56.0 – Merging and Cross-study Validation of Gene Expression data

MergeMaid 2.56.0

:: DESCRIPTION

The functions in MergeMaid are intended for cross-study comparison of gene expression array data.

::DEVELOPER

Division of Biostatistics and Bioinformatics – Johns Hopkins University Oncology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 MergeMaid

:: MORE INFORMATION

Citation:

Stat Appl Genet Mol Biol. 2004;3:Article29. Epub 2004 Oct 31.
MergeMaid: R tools for merging and cross-study validation of gene expression data.
Cope L1, Zhong X, Garrett E, Parmigiani G.

gffcompare 0.9.6f – Comparing, Annotating, Merging and Tracking Transcripts in GFF files

gffcompare 0.9.6f

:: DESCRIPTION

gffcompare is a program for comparing, annotating, merging and tracking transcripts in GFF(General Feature Format) files

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 gffcompare

:: MORE INFORMATION

LPmerge 1.6 – Merging Linkage Maps by Linear programming

LPmerge 1.6

:: DESCRIPTION

LPmerge is an R package for building consensus maps across multiple populations through linear programming (LP).

::DEVELOPER

Endelman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

 LPmerge

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 1;30(11):1623-4. doi: 10.1093/bioinformatics/btu091. Epub 2014 Feb 14.
LPmerge: an R package for merging genetic maps by linear programming.
Endelman JB1, Plomion C2.

modelBorgifier 1.0 – Comparing and Merging Metabolic Models

modelBorgifier 1.0

:: DESCRIPTION

Matching and comparison of genome-scale reconstructions and models are facilitated by modelBorgifier. It reconciles models in light of different annotation schemes, allowing diverse models to become useful for synchronous investigation.

::DEVELOPER

BRAIN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • MATLAB
  • COBRA Toolbox

:: DOWNLOAD

 modelBorgifier

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 1;30(7):1036-8. doi: 10.1093/bioinformatics/btt747. Epub 2013 Dec 25.
Assimilating genome-scale metabolic reconstructions with modelBorgifier.
Sauls JT1, Buescher JM.

SeqPrep 1.1 – Tripping Adaptors and/or Merging paired reads with overlap into Single Reads.

SeqPrep 1.1

:: DESCRIPTION

SeqPrep is a program to merge paired end Illumina reads that are overlapping into a single longer read. It may also just be used for its adapter trimming feature without doing any paired end overlap.

:: DEVELOPER

John St. John

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  SeqPrep

:: MORE INFORMATION