botond-sipos Goto Github PK

biogo

biogo is a bioinformatics library for Go

csvtk

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

ensembl-compara

The Ensembl Compara Perl API and SQL schema

hammerpede

A package for training strand-specific profile HMMs for primer sets from real Nanopore data

isonclust2

A tool for de novo clustering of long transcriptomic reads

manuscript-pat

PAT-seq manuscript

paper-ng-sam

Pipeline for simulating NG-SAM experiments

paper-pat-seq

paper-rlsim

Analysis pipeline for assesing biasing factors in Illumina RNA-seq protocols through realistic simulations

pcrcoal

pcrcoal is an R package implementing the coalescent approach to PCR simulation developed by Weiss and von Haeseler (NAR, 1997)

phylosim

An R package for the Monte Carlo simulation of sequence evolution

pinfish

Tools to annotate genomes using long read transcriptomics data

pipeline-nanopore-denovo-isoforms

Pipeline for de novo clustering of long transcriptomic reads

pipeline-nanopore-ref-isoforms

Pipeline for annotating genomes using long read transcriptomics data with stringtie and other tools

pipeline-polya-diff

Pipeline for testing shifts in poly(A) tail lengths estimated by nanopolish

pipeline-polya-ng

Pipeline for calling poly(A) tail lengths from nanopore direct RNA data using nanopolish

pipeline-transcriptome-de

Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads

pychopper

A tool to identify, orient, trim and rescue full length cDNA reads

rlsim

A package for simulating RNA-seq library preparation with parameter estimation

seqkit

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

simcopy

An R package simulating the evolution of copy number profiles along a tree

spliced_bam2gff

thist

A go package for generating online histograms and plotting them in the terminal and PDFs

wub

Tools and software library developed by the ONT Applications group