STAN 1.4.0 – STrand-specific ANnotation of Genomic data

STAN 1.4.0

:: DESCRIPTION

STAN implements bidirectional Hidden Markov Models (bdHMM), which are designed for studying directed genomic processes, such as gene transcription, DNA replication, recombination or DNA repair by integrating genomic data.

::DEVELOPER

Tresch Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • R

:: DOWNLOAD

  STAN

:: MORE INFORMATION

Citation

Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle.
Zacher B, Lidschreiber M, Cramer P, Gagneur J, Tresch A.
Mol Syst Biol. 2014 Dec 19;10:768. doi: 10.15252/msb.20145654.

RNASeqBrowser V2 – A Genome Browser for Strand Specific RNAseq Reads

RNASeqBrowser V2

:: DESCRIPTION

RNASeqBrowser is a visualization tool that incorporates and extends the functionality of the UCSC genome browser. For example, RNASeqBrowser simultaneously displays read coverage, SNPs, InDels and raw read tracks with other BED and wiggle tracks — all being dynamically built from the BAM file.

::DEVELOPER

Systems Biology of Gene Regulatory Elements

:: SCREENSHOTS

RNASeqBrowser

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  •  java

:: DOWNLOAD

  RNASeqBrowser

:: MORE INFORMATION

CRISPRDirection 1.0 – Accurate Computational Prediction of Transcribed Strand of CRISPR non-coding RNAs

CRISPRDirection 1.0

:: DESCRIPTION

CRISPRDirection is an algorithm that accurately predicts the strand of the resulting crRNAs.

::DEVELOPER

Dr Chris Brown’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • Java

:: DOWNLOAD

 CRISPRDirection

:: MORE INFORMATION

Citation:

Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs.
Biswas A, Fineran PC, Brown CM.
Bioinformatics. 2014 Jul 1;30(13):1805-13. doi: 10.1093/bioinformatics/btu114.

changePedStrand – Change Strand for a Pedigree file

changePedStrand

:: DESCRIPTION

changePedStrand is a sfotware which Changes Strand (by base pairing) for a Pedigree file.

::DEVELOPER

Yun Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 changePedStrand

:: MORE INFORMATION