ImageJ macros and scripts written at the imaging facility MRI

transcriptome-wide profiling 3'UTR splicing events using conventional RNA sequencing data

Tandem Repeats Finder: a program to analyze DNA sequences

(Not Offical) BBMap short read aligner, and other bioinformatic tools.

htop - an interactive process viewer

Bioconductor package "ballgown", devel version. Isoform-level differential expression analysis in R.

Tool for the detection and quantification of alternative splicing events from RNA-Seq data.

Deep-learning Augmented RNA-seq analysis of Transcript Splicing

Pilon is an automated genome assembly improvement and variant detection tool

Signal-level algorithms for MinION data

Reference-guided transcript discovery and quantification for long read RNA-Seq data

A single molecule sequence assembler for genomes large and small.

H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

MarginPolish: Graph based assembly polishing

HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommended).

A *fast* tool for BAM/CRAM quality evaluation, intended for long reads

adapter trimmer for Oxford Nanopore reads

Filtering and trimming of long read sequencing data

Full-Length Alternative Isoform analysis of RNA

Open source code for AlphaFold 2.

A versatile pairwise aligner for genomic and spliced nucleotide sequences

TCGAbiolinks

TransDecoder source

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

DETONATE: DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation

Code for running RFdiffusion

de novo assembly of RNA-seq data using ABySS

Trinity RNA-Seq de novo transcriptome assembly