smaegol
I am interested in the analysis of all kinds of NGS data, from metagenomics and bacterial genomics, to transcriptomics, TAILseq and long-read sequencing data
International Institute of Molecular and Cell BIologyWarsaw, Poland
Pinned Repositories
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
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)
nanotail
R package for visualization and exploratory analysis of Oxford Nanopore direct RNA seq based polyA predictions
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
scripts
various scripts used in routine bioinfo work
smaegol's Repositories
smaegol/PlasFlow
Software for prediction of plasmid sequences in metagenomic assemblies
smaegol/nanotail
R package for visualization and exploratory analysis of Oxford Nanopore direct RNA seq based polyA predictions
smaegol/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)
smaegol/laccases
smaegol/bioconda-recipes
Conda recipes for the bioconda channel.
smaegol/scripts
various scripts used in routine bioinfo work
smaegol/blastr
R wrapper for NCBI's blast
smaegol/d3pendr
Differential 3' end analysis
smaegol/DeepLearn
Implementation of research papers on Deep Learning+ NLP+ CV in Python using Keras, Tensorflow and Scikit Learn.
smaegol/dtaidistance
Time series distances: Dynamic Time Warping (fast DTW implementation in C)
smaegol/flair
Full-Length Alternative Isoform analysis of RNA
smaegol/hts-specs
Specifications of SAM/BAM and related high-throughput sequencing file formats
smaegol/lapa
Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.
smaegol/minion_qc
Quality control for MinION sequencing data
smaegol/NA12878
Data and analysis for NA12878 genome on nanopore
smaegol/nano_scripts
smaegol/nanopolish
Signal-level algorithms for MinION data
smaegol/ninetails
An R package for finding non-adenosine residues in poly(A) tails of ONT direct RNA sequencing reads
smaegol/ont2cram
Oxford Nanopore HDF/Fast5 to CRAM conversion tool
smaegol/polya_browser
polyA_browser
smaegol/poreduck
A comprehensive toolkit for running Oxford Nanopore's MinION
smaegol/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 ;)
smaegol/quarto-web
Quarto website
smaegol/raceseq_scripts
Various scripts for use in raceseq analysis
smaegol/siscreenr
high throughput screening analysis package
smaegol/smaegol.github.io
smaegol/tailfindr
An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
smaegol/TALON
Technology agnostic long read analysis pipeline for transcriptomes
smaegol/testpage
smaegol/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.