Tag: Isoform

NLDMseq – Expression Calculation at both Gene and Isoform levels from RNA-seq data given a Reference Transcriptom

NLDMseq

:: DESCRIPTION

NLDMseq is a bioinformatics tool for expression calculation at both gene and isoform levels from RNA-seq data by considering isoform- and exon-specific read sequencing rate.

::DEVELOPER

Xuejun Liu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python

:: DOWNLOAD

 NLDMseq

:: MORE INFORMATION

Citation

Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate.
Liu X, Shi X, Chen C, Zhang L.
BMC Bioinformatics. 2015 Oct 16;16(1):332. doi: 10.1186/s12859-015-0750-6.

MMSEQ 1.0.2 – Isoform Expression Estimation using Multi-mapping RNA-seq reads

MMSEQ 1.0.2

:: DESCRIPTION

MMSEQ deconvolves the mapping of reads to multiple transcripts (isoforms or haplotype-specific isoforms). The software can take into account non-uniform read generation and works with paired-end reads.

::DEVELOPER

Dr Ernest Turro

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MMSEQ

:: MORE INFORMATION

Citation

Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.
Turro E, Su SY, Gonçalves Â, Coin LJ, Richardson S, Lewin A.
Genome Biol. 2011;12(2):R13. Epub 2011 Feb 10.

IQSeq 1.0 – Isoform Quantification with RNA-seq data

IQSeq 1.0

:: DESCRIPTION

IQSeq is a tool for isoform quantification with RNA-seq data. Given isoform annotation and alignment of RNA-seq reads, it will use an EM algorithm to infer the most probable expression level for each isoform of a gene.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 IQSeq

:: MORE INFORMATION

Citation:

Jiang Du, Jing Leng, Lukas Habegger, Andrea Sboner, Drew McDermott, Mark Gerstein.
“IQSeq: Integrated Isoform Quantification Analysis Based on Next-generation Sequencing”
PLoS ONE 7(1): e29175. doi:10.1371/journal.pone.0029175