ALSYSTA 1.07 Beta – Analysis of different Aspects of Biological Systems

ALSYSTA 1.07 Beta

:: DESCRIPTION

ALSYSTA (BioSystAnSe) is a software suite that includes a series of tools for the analysis of different aspects of biological systems, such as the expression phenotype and the metabolic flux profiles of cells, as well as various tools to search web based databases.

::DEVELOPER

The Bioinformatics & Metabolic Engineering Laboratory, Massachusetts Institute of Technology

:: SCREENSHOTS

ALSYSTA

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 ALSYSTA

:: MORE INFORMATION

sicegar 0.2.3 – Analysis of Single-cell Viral Growth Curves

sicegar 0.2.3

:: DESCRIPTION

sicegar is an R package for the analysis of single cell virology growth curves.

::DEVELOPER

Claus Wilke’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

sicegar

:: MORE INFORMATION

Citation

PeerJ, 6, e4251 2018 Jan 16 eCollection 2018
Sicegar: R Package for Sigmoidal and Double-Sigmoidal Curve Fitting
M Umut Caglar , Ashley I Teufel , Claus O Wilke

Biogrep 1.0 – Optimised Version of Grep for matching Patterns against Sequences

Biogrep 1.0

:: DESCRIPTION

Biogrep is a tool designed to quickly match large sets of patterns against biosequence databases and is optimized for multi–processor computers. Biogrep uses standard POSIX extended regular expressions and can divide the pattern–matching task between a user–specified number of processors.

::DEVELOPER

The Bioinformatics & Metabolic Engineering Laboratory, Massachusetts Institute of Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Biogrep

:: MORE INFORMATION

Citation:

Kyle Jensen et. al. (2002);
Biogrep: A multi-threaded pattern matcher for large pattern sets

mspire 0.10.8 – Mass Spectrometry Proteomics in Ruby

mspire 0.10.8

:: DESCRIPTION

Mspire is a full featured library for working with mass spectrometry data, particularly proteomic, metabolomic and lipidomic data sets. It aims to be fast, robust, and beautiful.

::DEVELOPER

Prince Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Ruby

:: DOWNLOAD

 mspire

:: MORE INFORMATION

Citation

Prince JT, Marcotte EM.
mspire: mass spectrometry proteomics in Ruby.
Bioinformatics. 2008 Dec 1;24(23):2796-7.

DANPOS 2.2.2 – Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing

DANPOS 2.2.2

:: DESCRIPTION

DANPOS is designed for genome-wide comparative analysis of nucleosome maps. It detect single-nucleotide-resolution change in positions(location), enrichment (occupancy), and fuzziness (phasing, positioning) of each nucleosome unit.

::DEVELOPER

Wei Li’s Computational Epigenomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 DANPOS

:: MORE INFORMATION

Citation:

Genome Res. 2013 Feb;23(2):341-51. doi: 10.1101/gr.142067.112. Epub 2012 Nov 28.
DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing.
Chen K, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S, He X, Li W.

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.

spkTools 1.43.0 – Collection of Functions to Analyze Microarray Spike-in data

spkTools 1.43.0

:: DESCRIPTION

spkTools contains functions that can be used to compare expression measures on different array platforms.

::DEVELOPER

Matthew N. McCall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R package
  • Bioconductor

:: DOWNLOAD

 spkTools

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2008 Oct;36(17):e108. doi: 10.1093/nar/gkn430. Epub 2008 Aug 1.
Consolidated strategy for the analysis of microarray spike-in data.
McCall MN, Irizarry RA.

MACE 1.2 – Model-based Analysis of ChiP-exo

MACE 1.2

:: DESCRIPTION

MACE is a novel analysis framework to detect two binding borders of protein-DNA interactions from ChIP-exo data.

::DEVELOPER

Wei Li’s Computational Epigenomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 MACE

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Nov 10;42(20):e156. doi: 10.1093/nar/gku846. Epub 2014 Sep 23.
MACE: model based analysis of ChIP-exo.
Wang L, Chen J, Wang C, Uusküla-Reimand L, Chen K, Medina-Rivera A, Young EJ, Zimmermann MT, Yan H, Sun Z, Zhang Y, Wu ST, Huang H, Wilson MD, Kocher JP, Li W

BioAnalyzer 2100 – Analysis of BioAnalyzer data

BioAnalyzer 2100

:: DESCRIPTION

The Agilent 2100 BioAnalyzer is a nanofluidics device that preforms size fractionation and quantification of small samples of DNA, RNA, or Protein. In addition, the BioAnalyzer is able to preform flow cytometry on small numbers of cells.

::DEVELOPER

the MIT BioMicro Center

:: SCREENSHOTS

BioAnalyzer

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 BioAnalyzer

:: MORE INFORMATION

nondetects 2.16.0 – Model and Impute non-detects in qPCR data

nondetects 2.16.0

:: DESCRIPTION

nondetects is a suit of methods to model and impute non-detects in the results of qPCR experiments.

::DEVELOPER

Matthew N. McCall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R package
  • Bioconductor

:: DOWNLOAD

 nondetects

:: MORE INFORMATION

Citation

On non-detects in qPCR data.
McCall MN, McMurray HR, Land H, Almudevar A.
Bioinformatics. 2014 Apr 23. pii: btu239