Tag: Data

FCAnalysis 1.0.0 – Independent Component Analysis for Mining Gene Expression Data

FCAnalysis 1.0.0

:: DESCRIPTION

FCAnalysis is the first package contains the R code for extracting fundamental components as well as for analyzing new datasets in terms of the human fundamental components we identified. The second package contains lists of genes in the dominant modules for our 423 human fundamental components.

::DEVELOPER

FCAnalysis Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 FCAnalysis

:: MORE INFORMATION

Citation

Engreitz JM, Daigle Jr. BJ, Marshall JJ, Altman RB.
Independent component analysis: mining microarray data for fundamental human gene modules.
Journal of Biomedical Informatics. 2010 (in revision). (2010)

GPeriodic 2.0.10 – Look up Data of Elements from the Periodic Table

GPeriodic 2.0.10

:: DESCRIPTION

GPeriodic is a program for looking up data of elements from the periodic table. This program also features a non-graphical interface.

::DEVELOPER

Jonas Frantz , Kyle R. Burton.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

GPeriodic

:: MORE INFORMATION

Software on this page are free software released under the GNU General Public License.

G3data 1.5.4 – Extract Data from Graphs

G3data 1.5.4

:: DESCRIPTION

g3data is used for extracting data from graphs. In publications graphs often are included, but the actual data is missing. g3data makes the extracting process much easier.

::DEVELOPER

Jonas Frantz, Paul Novak

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • gtk+

:: DOWNLOAD

G3data

:: MORE INFORMATION

g3data is distributed under the GNU General Public License (GPL), as described in the ‘COPYING’ file.

PCAGEN 1.2.1 – Perform Principal Component Analysis on Gene Frequency Data

PCAGEN 1.2.1

:: DESCRIPTION

PCAGEN is a computer package for Windows which performs Principal Component Analysis (PCA) on gene frequency data. Graphical ordinations of samples are provided and graphs can be saved. Using randomizations, the program also tests the significance of total inertia as well as individual axes inertia.

::DEVELOPER

Jérôme Goudet.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

PCAGEN

:: MORE INFORMATION

YCDMA 3.1.1 – Manage Microsatellite Data

YCDMA 3.1.1

:: DESCRIPTION

YCDMA (Y Chromosome Data Management) is designated to manage microsatellite data (mono- and bi-allelic).In order to reflect the hierarchical organization of an experiment, samples may be arranged into user-defined populations and populations into groups.Data defined in an experiment may be exported in one of the following formats (allowing their use in the corresponding softwares) :

ARLEQUIN
DISPAN
GENEPOP
MICROSAT
MIGRATE
NJBAFD

::DEVELOPER

Daniel Montagnon PhD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

YCDMA

:: MORE INFORMATION

If you download and use this software please register to be informed for new release and modifications.

DnaSP 5.10.01 – Analysis of Nucleotide Polymorphism from Aligned DNA Sequence Data

DnaSP 5.10.01

:: DESCRIPTION

DnaSP （DNA Sequence Polymorphism） is a software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters.

::DEVELOPER

J. Rozas, P. Librado, J. C. Sánchez-DelBarrio, X. Messeguer and R. Rozas
Molecular Evolutionary Genetics Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

DnaSP

:: MORE INFORMATION

Citation

Librado, P. and Rozas, J. 2009.
DnaSP v5: A software for comprehensive analysis of DNA polymorphism data.
Bioinformatics 25: 1451-1452 | doi: 10.1093/bioinformatics/btp187.

MFI 3.4kb8 – Analysis of Flow Cytofluorometry Data

MFI 3.4kb8

:: DESCRIPTION

MFI (Median Fluorescence Intensity ) is Software for Analysis of Flow Cytofluorometry Data. MFI was created to obtain corrected median fluorescence intensities quickly from large numbers of flow cytometry listmode data files.

::DEVELOPER

Eric Martz

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

MFI ; Source Code

:: MORE INFORMATION

Development of the MFI program stopped in 1996 at version 3.4kb8. No further enhancements will be released by MFI’s author Eric Martz.

BioGridRunner 2002 – Bioinformatics Data Grid Application

BioGridRunner 2002

:: DESCRIPTION

BioGridRunner is a distributed computing application for bioinformatics, incorporating directory services (data and software), grid computing methods (security, authentication, data transport and remote jobs), and gene sequence and genomic data processing methods.

::DEVELOPER

Don Gilbert at Indiana University

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

BioGridRunner

:: MORE INFORMATION

This is an experimental program. No warranty is made for its operations. It includes methods which view and manipulate files, on your computer and others. The author believes it is safe for testing, but cannot promise use will not damage your files or data inadvertantly.

GenePublisher 1.03 – Analysis of DNA Microarray Data

GenePublisher 1.03

:: DESCRIPTION

GenePublisher performs automated data analysis from gene expression experiments on a number of different platforms. This server accepts gene tables or Affymetrix CEL files as input, performs numerical and statistical analysis, links the results to various databases, and returns a report of the results. The input data is deleted immediately upon completion of the analysis unless you select the database option below.

::DEVELOPER

CBS (Center for Biological Sequence Analysis) at Technical University of Denmark

:: SCREENSHOTS

:: REQUIREMENTS

  • web browser

:: MORE INFORMATION

Input restrictions:

  • The input CEL files must be compressed with gzip (available from www.gzip.org) and cannot be more than 30 Mbytes in total size. That corresponds to 12 HuGeneFL chips, 10 HG_U95A chips, 22 Focus chips, 8 HG-U133A chips, and so on. The maximum number of chips accepted on this web server is currently 12. There is another server without input restrictions.
  • Avoid using characters _, &, %, # in the input as they may interfere with analysis.

For publication of results, please cite:

GenePublisher: Automated Analysis of DNA Microarray Data.
Knudsen, S., Workman, C., Sicheritz-Ponten, T., and Friis, C.
Nucleic Acids Research. Vol. 31, No. 13 3471-3476.

Exit mobile version