FuSeq 1.1.4 – Discover Fusion Genes from paired-end RNA Sequencing data

FuSeq 1.1.4

:: DESCRIPTION

FuSeq discovers fusion genes based on quasi-mapping to quickly map the reads, extract initial candidates from split reads and fusion equivalence classes of mapped reads, and finally apply multiple filters and statistical tests to get the final candidates.

::DEVELOPER

PROF. YUDI PAWITAN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

FuSeq

:: MORE INFORMATION

Citation

Vu TN, Deng W, Trac QT, Calza S, Hwang W, Pawitan Y.
A fast detection of fusion genes from paired-end RNA-seq data.
BMC Genomics. 2018 Nov 1;19(1):786. doi: 10.1186/s12864-018-5156-1. PMID: 30382840; PMCID: PMC6211471.

RNASeqBias 1.0 – Bias Detection and Correction in RNA-Sequencing Data

RNASeqBias 1.0

:: DESCRIPTION

RNASeqBias contains functions and sample data for detecting and correcting for biases in gene expression levels from RNA-Seq experiments. Considered bias factors are gene length, GC content and dinucleotide frequencies. Principal component analysis on GC content and dinucleotide frequencies are first performed, and the resulting principal components and gene length were used as covariates to fit a generalized additive model with smoothing spline on gene expression levels as response. The package also have codes to generate bias plots before and after bias correction, and to compare with other quantitative platforms.

::DEVELOPER

Zhao Hongyu’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 RNASeqBias

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Jul 19;12:290. doi: 10.1186/1471-2105-12-290.
Bias detection and correction in RNA-Sequencing data.
Zheng W1, Chung LM, Zhao H.

DeAnnIso – Detection and Annotation of IsomiR from small RNA sequencing data

DeAnnIso

:: DESCRIPTION

DeAnnIso, is an online tool, that is designed for Detection and Annotation of IsomiR from small RNA sequencing data.

::DEVELOPER

BioStaCs group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

DeAnnIso: a tool for online detection and annotation of isomiRs from small RNA sequencing data.
Zhang Y, Zang Q, Zhang H, Ban R, Yang Y, Iqbal F, Li A, Shi Q.
Nucleic Acids Res. 2016 May 13. pii: gkw427