Perugolate's Stars
wdecoster/nanopack
An overview of all nanopack tools
lbcb-sci/herro
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).
open2c/bioframe
Genomic interval operations on Pandas DataFrames
conchoecia/odp
oxford dot plots
marbl/parsnp
Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
vsbuffalo/granges
A Rust library and command line tool for working with genomic ranges and their data.
pinin4fjords/shinyngs
Shiny apps for NGS etc based on reusable components created using Shiny modules
COMBINE-lab/oarfish
long read RNA-seq quantification
a-slide/NanoCount
EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
YingZhou001/Immuannot
Immuological gene typing and annotation for genome assembly
HipSTR-Tool/HipSTR
Genotype and phase short tandem repeats using Illumina whole-genome sequencing data
InsightRX/clinPK
Equations and tools for clinical pharmacokinetics
jts/smrest
Tumour-only somatic mutation calling using long reads
larssnip/micropan
R package for microbial pangenomics
rafalab/excessmort
R package for estimating excess deaths from daily count data
treangenlab/Olivar
Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens
j-a-thia/genomalicious
A smorgasbord of R functions for population genomic analyses
PROBIC/mGEMS
mGEMS Genomic epidemiology with mixed samples
marbl/gingr
PROBIC/mSWEEP
mSWEEP High-resolution sweep metagenomics using fast probabilistic inference
vsbuffalo/slimflow
marbl/harvest-tools
THJlab/seqNdisplayR
Produce reproducible, pretty genome coverage plots using highly customizable layout and coverage normalization, batch correction etc.
bio-ontology-research-group/deepgometa
tamas-ferenci/MortalityPrediction
MortalityPrediction
cednotsed/vertebrate_host_jumps
andrewmoles2/training-resources
Repository of various useful resources for training
djwooten/natcomms-musyc2021
pczuppon/AMRWithinHost
Code to reproduce the results of the manuscript "Stochastic within-host dynamics of antibiotic resistance: Resistant survival probability, size at the end of treatment and carriage time after treatment"
JSHuisman/Recorder