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acfs

A pipeline for de novo circRNA identification

circexplorer2

circular RNA analysis toolset

clear

direct comparison of circular and linear RNA expression

compbio-base

A C# solution with projects containing utiliy classes that are used e.g. in MaxQuant and Perseus

debks

a tool to detect differentially expressed circular RNA

find_circ2

Find circRNAs in RNA-seq data.

flamanalysis

Data Analysis For FLAM-Seq Third Generation RNA Sequencing

freecodecamp

The https://FreeCodeCamp.com open source codebase and curriculum. Learn to code and help nonprofits.

knife

Known and Novel IsoForm Explorer. Statistically based splicing detection for circular and linear isoforms

mirdeep2

Discovering known and novel miRNAs from small RNA sequencing data

msgfplus

MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.

pdfapi2

Facilitates the creation and modification of PDF files in Perl

perseus-plugins

The perseus software for the statistical analysis of omics data (http://www.perseus-framework.org/) has a plugin architecture. Here you find the code necessary to develop your own plugins.

ptesfinder_v1

pybedtools

Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)

pysam

Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.

sailfish-cir

a pipeline for quantification of circular RNA.

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

seqtk

Toolkit for processing sequences in FASTA/Q formats

star

RNA-seq aligner

starchip

Detection of Circular RNA and Fusions from RNA-Seq

tensorflowsharp

TensorFlow API for .NET languages

trimgalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

tximport

Import and summarize transcript-level estimates for gene-level analysis