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article-downloader

Uses publisher APIs to programmatically retrieve large amounts of scientific journal articles for text mining.

ayb2

AYB2 -- All Your Base version 2. A base caller for the Illumina platform

bioconda-recipes

Conda recipes for the bioconda channel.

biostrext

Extension to Biostrings R package

blastr

R wrapper for NCBI's blast

cheatsheets

RStudio Cheat Sheets

d3pendr

Differential 3' end analysis

datamining

Lecture notes for Advances in Data Mining

deeplearn

Implementation of research papers on Deep Learning+ NLP+ CV in Python using Keras, Tensorflow and Scikit Learn.

dtaidistance

Time series distances: Dynamic Time Warping (fast DTW implementation in C)

flair

Full-Length Alternative Isoform analysis of RNA

hts-specs

Specifications of SAM/BAM and related high-throughput sequencing file formats

laccases

lapa

Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.

line_1_race_seq_analysis

Scripts and data used during the analysis of LINE-1 RACE seq tail-seq output, for the publication "Uridilation by TUT4/7 restricts retrotransposition of human LINE-1"s (Warkocki et al 2018, Cell, available at https://doi.org/10.1016/j.cell.2018.07.022)

markdown-cheatsheet

Markdown Cheatsheet for Github Readme.md

megahit

MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

minion_qc

Quality control for MinION sequencing data

na12878

Data and analysis for NA12878 genome on nanopore

nano_scripts

nanopolish

Signal-level algorithms for MinION data

nanotail

R package for visualization and exploratory analysis of Oxford Nanopore direct RNA seq based polyA predictions

ninetails

An R package for finding non-adenosine residues in poly(A) tails of ONT direct RNA sequencing reads

ont2cram

Oxford Nanopore HDF/Fast5 to CRAM conversion tool

parsing-repeatmasker-outputs

Few scripts facilitating the extraction of info from Repeat Masker .out files

plasflow

Software for prediction of plasmid sequences in metagenomic assemblies

plasflow_models

Additional models used during development of PlasFlow

plasflow_processing

Scripts used during the development of PlasFlow

polya_browser

polyA_browser

poreduck

A comprehensive toolkit for running Oxford Nanopore's MinION