smaegol

PlasFlow

Software for prediction of plasmid sequences in metagenomic assemblies

nanotail

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

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)

laccases

bioconda-recipes

Conda recipes for the bioconda channel.

scripts

various scripts used in routine bioinfo work

blastr

R wrapper for NCBI's blast

d3pendr

Differential 3' end analysis

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

lapa

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

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

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

polya_browser

polyA_browser

poreduck

A comprehensive toolkit for running Oxford Nanopore's MinION

Probabilistic-Programming-and-Bayesian-Methods-for-Hackers

aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)

quarto-web

Quarto website

raceseq_scripts

Various scripts for use in raceseq analysis

siscreenr

high throughput screening analysis package

smaegol.github.io

tailfindr

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

TALON

Technology agnostic long read analysis pipeline for transcriptomes

testpage

Theano

Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. It can use GPUs and perform efficient symbolic differentiation.