Tag: Quantifying

nagnag 1.0.3 – Identifyng and Quantifying NAGNAG Alternative Splicing

nagnag 1.0.3

:: DESCRIPTION

nagnag is an R package for NAGNAG alternative splicing

:: DEVELOPER

Dr. Xiaoyong Sun, Genomics and Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows
  • R

:: DOWNLOAD

 nagnag

:: MORE INFORMATION

Citation

Biomed Res Int. 2014;2014:736798. doi: 10.1155/2014/736798. Epub 2014 Jun 5.
Computational evidence of NAGNAG alternative splicing in human large intergenic noncoding RNA.
Sun X, Lin SM, Yan X

nagnag: Identification and quantification of NAGNAG alternative splicing using RNA-Seq data.
Yan X, Sablok G, Feng G, Ma J, Zhao H, Sun X.
FEBS Lett. 2015 May 27. pii: S0014-5793(15)00423-8. doi: 10.1016/j.febslet.2015.05.029

JODA 1.33.0 – Quantifying Gene Deregulation using Knowledge

JODA 1.33.0

:: DESCRIPTION

JODA (Joint deregulation analysis) proves advantageous over separate analysis of the cell populations and analysis without incorporation of knowledge.

:: DEVELOPER

JODA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 JODA

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Jun 21;12:249. doi: 10.1186/1471-2105-12-249.
Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data.
Szczurek E1, Markowetz F, Gat-Viks I, Biecek P, Tiuryn J, Vingron M.

ASprofile – Extracting, Quantifying and Comparing Alternative Splicing (AS) Events from RNA-seq data

ASprofile

:: DESCRIPTION

ASprofile is a suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data.

::DEVELOPER

Center for Computational Biology , Johns Hopkins University School of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  ASprofile

:: MORE INFORMATION

ERANGE 4.0a – Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq

ERANGE 4.0a

:: DESCRIPTION

The functions of ERANGE are to (i) assign reads that map uniquely in the genome to their site of origin and, for reads that match equally well to several sites (‘multireads’), assign them to their most likely site(s) of origin; (ii) detect splice-crossing reads and assign them to their gene of origin; (iii) organize reads that cluster together, but do not map to an already known exon, into candida

::DEVELOPER

the Wold Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ERANGE

:: MORE INFORMATION

Citation

Nat Methods. 2008 Jul;5(7):621-8. Epub 2008 May 30.
Mapping and quantifying mammalian transcriptomes by RNA-Seq.
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B.

 

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