stanikae

h3ameta

H3ABioNet Metagenomics Workflow

AGAT

Another Gtf/Gff Analysis Toolkit

ALPPACA

A tooL for Prokaryotic Phylogeny And Clustering Analysis

awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

Calculate-Haplotype-Frequencies

This script calculates allelic and genotypic frequencies, as well as perform Fisher's Exact Test to compare representation of genotypes and alleles in different sample groups

Extract-haplotype-sequences

jekesa

Jekesa (Illuminate) is an automated bash pipeline for bacterial whole genome assembly and typing using Illumina paired-end sequencing data.

lncRNA-analysis

miRNA-analysis

Pipeline for miRNA profiling, including read mapping, multi-mapped read correction and read counting

stanikae/AGAT

Another Gtf/Gff Analysis Toolkit

stanikae/ALPPACA

A tooL for Prokaryotic Phylogeny And Clustering Analysis

stanikae/awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

stanikae/broad-fungalgroup

Broad Fungal Genomics group scripts

stanikae/clockwork

CRyPTIC data processing pipelines

stanikae/Extract-haplotype-sequences

stanikae/book-compgenomr

stanikae/c9-python-getting-started

Sample code for Channel 9 Python for Beginners course

stanikae/compare_genomes

A comparative genomics workflow using Nextflow, conda, Julia and R

stanikae/CoverM

Read coverage calculator for metagenomics

stanikae/eca-bioinf-handbook

Lecture notes/book in progress on computing for conservation genomics

stanikae/emmtyper

emm Automatic Isolate Labeller

stanikae/FastANI

Fast Whole-Genome Similarity (ANI) Estimation

stanikae/Freyja

Depth-weighted De-Mixing

stanikae/hAMRonization

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

stanikae/happy-git-with-r

Using Git and GitHub with R, Rstudio, and R Markdown

stanikae/kingfisher-download

Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

stanikae/mycosnp-nf

CDCgov/mycosnp-nf

stanikae/nextflow_cheatsheet

Tips for Nextflow and cheatsheet for channel operation

stanikae/patterns

A curated collection of Nextflow implementation patterns

stanikae/phytools

stanikae/Practical-Computing-and-Bioinformatics

A minimal example of using bookdown to write a book for Chapman & Hall/CRC

stanikae/PreProcSEQ

Quality control pipeline and pre-processing of data from RNA-Seq

stanikae/seqera-kit

Python implementation for automated pipeline launching through Tower CLI (beta)

stanikae/seqtk

Toolkit for processing sequences in FASTA/Q formats

stanikae/snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment

stanikae/vamb

Variational autoencoder for metagenomic binning

stanikae/viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples

stanikae/viroprofiler

A containerized bioinformatics pipeline for viral metagenomic data analysis

stanikae/visNetwork

R package, using vis.js library for network visualization