Uncategorized tools for RNA sequencing analysis.
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digitagCT

An integrated bioinformatics approach that combines DGE tags, RNA-Seq, tiling array expression data and species-comparison to explore new transcriptional regions and their specific biological features, particularly...

genCAT

Gene's Comprehensive Annotation Tool
It is an open platform that allows users to incorporate as many datasets (concepts) as possible to annotate the input gene list, as long as these datasets are prepared in bigwig, BED, BAM/SAM formats.

GSAASeqSP

A toolset for genome-wide gene set association analysis of sequence count data.

NASTIseq

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data.

Parseq

A statistical approach for transcription landscape reconstruction at a basepair resolution from RNA Seq read counts.

piPipes

A coordinated set of pipelines, 'piPipes', to analyze piRNA and transposon-derived RNAs from a variety of high-throughput sequencing libraries, including small RNA, RNA, degradome or 7-methyl guanosine cap analysis of...

PLEK

predictor of long non-coding RNAs and messenger RNAs based on an improved k-mer scheme
An alignment-free tool which uses a computational pipeline based on an improved k-mer scheme and a support vector machine (SVM) algorithm to distinguish lncRNAs from messenger RNAs (mRNAs), in the absence of genomic...

UTR

A change-point model for detecting 3'UTR changes by RNA-Seq.

XSAnno

A computational framework that integrates previous approaches with multiple filters to improve the accuracy of inter-species transcriptome comparisons.