Tag: calculating

RaTrav 20130916 – Calculating Mean First Passage Times using Hill’s and Monte Carlo algorithms

RaTrav 20130916

:: DESCRIPTION

RaTrav tool was designed to support computational biology studies where mean first-passage times (MFPTs) between initial and single, or multiple, final states in network-like systems are used. Two methods are made available for which their efficiency is strongly dependent on the topology of the defined network. The user is required to prepare a text file with the structure of a given network, along with some additional basic parameters.

::DEVELOPER

Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 RaTrav

:: MORE INFORMATION

Citation

M. Torchala, P. Chelminiak and P. A. Bates,
‘Mean first-passage time calculations: comparison of the deterministic Hill’s algorithm with Monte Carlo simulations‘,
Eur. Phys. J. B 85 116 (2012).

Myrna 1.2.3 – Cloud-scale Differential Gene Expression for RNA-seq

Myrna 1.2.3

:: DESCRIPTION

Myrna is a cloud computing tool for calculating differential gene expression in large RNA-seq datasets. Myrna uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization, and statistical testing. These tools are combined in an automatic, parallel pipeline that runs in the cloud (Elastic MapReduce in this case) on a local Hadoop cluster, or on a single computer, exploiting multiple computers and CPUs wherever possible.

::DEVELOPER

Ben Langmead, Kasper Hansen, and Jeffrey Leek

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R package
  • Bowtie

:: DOWNLOAD

  Myrna

:: MORE INFORMATION

Citation

Genome Biol. 2010;11(8):R83. doi: 10.1186/gb-2010-11-8-r83. Epub 2010 Aug 11.
Cloud-scale RNA-sequencing differential expression analysis with Myrna.
Langmead B, Hansen KD, Leek JT.

FamSeq 1.0.3 – Calculating Probability of Variants in Family-based Sequencing data

FamSeq 1.0.3

:: DESCRIPTION

FamSeq (Family-Based Sequencing) is a computational tool for calculating probability of variants in family-based sequencing data.

::DEVELOPER

Statistical Bioinformatics Lab, The University of Texas M. D. Anderson Cancer Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX/Windows
  • C++ Compiler

:: DOWNLOAD

   FamSeq

:: MORE INFORMATION

Citation

Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3985-90. doi: 10.1073/pnas.1222158110.
Rare variant detection using family-based sequencing analysis.
Peng G, Fan Y, Palculict TB, Shen P, Ruteshouser EC, Chi AK, Davis RW, Huff V, Scharfe C, Wang W.

mf2q – Calculating Scaled Q matrices from Mutation Counts using the DCFreq method

mf2q

:: DESCRIPTION

mf2q is a Python script calculating Q matrices scaled to give one expected substitution per unit time from mutation count data using the DCFreq method.

::DEVELOPER

Botond Sipos

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 mf2q

:: MORE INFORMATION

Citation

Kosiol C., Goldman N. (2005)
Different versions of the Dayhoff rate matrix.
Mol Biol Evol 22:193-199

LDDist 1.3.2 – Calculating LogDet Pair-wise Distances for Protein and Nucleotide Sequences

LDDist 1.3.2

:: DESCRIPTION

LDDist is a Perl module implemente in C++ that enables the user to calculate LogDet pair-wise genetic distances based on amino acid as well as DNA/RNA sequences

::DEVELOPER

Mikael Thollesson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/ Windows
  • Perl
  • C++ Compiler

:: DOWNLOAD

 LDDist

:: MORE INFORMATION

Citation

Bioinformatics. 2004 Feb 12;20(3):416-8. Epub 2004 Jan 22.
LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences.
Thollesson M.

rpkmforgenes.py – Calculating Gene Expression for RNA-Seq data

rpkmforgenes.py

:: DESCRIPTION

The python script rpkmforgenes.py is written for calculating gene expression for RNA-Seq data.

::DEVELOPER

Sandberg Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python

:: DOWNLOAD

 rpkmforgenes.py

:: MORE INFORMATION

Citation

Ramsköld D, Wang ET, Burge CB, Sandberg R (2009)
An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data.
PLoS Comput Biol 5(12): e1000598. doi:10.1371/journal.pcbi.1000598