quickly filter fastq files by matching sequences to a set of regex patterns

A statistical tool to detect differential alternative splicing events using single-cell RNA-seq

The Read Z-score (ReadZS) is a metric that summarizes the transcriptional state of a gene in a single cell.

single-cell clustering based on alternative splicing landscapes

Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/

Accurate, easy and integrated suit to compare RNA samples with different degradation levels, quantify decay rates per-transcript and correct for degradation-induced artifacts in differential gene/t…

iSofOrmS annoTAtoR pipeline

Near-optimal RNA-Seq quantification

An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.

Dynamics analysis of Alternative PolyAdenylation from long-reads RNA-seq

scLVM is a modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources, thereby allowing for the correction of confounding sources…

Graph Network for protein-protein interface including language model features

A geometric deep learning pipeline for predicting protein interface contacts. (ICLR 2022)

A deep-learning model for predicting RNA-binding capacity from protein interaction association context and protein sequence

LncADeep is an ab initio lncRNA identification and functional annotation tool based on deep learning

FEELnc : FlExible Extraction of LncRNA

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate set…

isoCirc

Convert and query IDs of circular RNAs from many different databases

Circr, a computational tool for the prediction of circRNA-miRNA associations.

A Linux Shell Handbook for Bioinformatician

Splicing Neo Antigen Finder (SNAF) is an easy-to-use Python package to identify splicing-derived tumor neoantigens from RNA sequencing data, it further leverages both deep learning and hierarchical…