Pinned Repositories
adegenet
adegenet: a R package for the multivariate analysis of genetic markers
annotation_pipeline_nextflow
Bacterial genome annotation and comparative analysis pipeline (for setup of chlamdb-type database)
auto_barcode
Extracts fastq reads for specified barcode(s) from one or multiple FASTQ files
Bandage
a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
bovine-graphs-mapping
Repository to reproduce results in the bovine graphs mapping paper
breakaway
Species richness with high diversity
brokenaxes
Create matplotlib plots with broken axes
calour
exploratory and interactive microbiome analyses based on heatmaps
cojac
Conifer
Calculate confidence scores from Kraken2 output
ditag's Repositories
ditag/adegenet
adegenet: a R package for the multivariate analysis of genetic markers
ditag/annotation_pipeline_nextflow
Bacterial genome annotation and comparative analysis pipeline (for setup of chlamdb-type database)
ditag/Bandage
a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
ditag/bovine-graphs-mapping
Repository to reproduce results in the bovine graphs mapping paper
ditag/breakaway
Species richness with high diversity
ditag/brokenaxes
Create matplotlib plots with broken axes
ditag/cojac
ditag/Conifer
Calculate confidence scores from Kraken2 output
ditag/corncob
Count Regression for Correlated Observations with the Beta-binomial
ditag/cutPrimers
curPrimers is a tool for trimming primer sequences from amplicon based NGS reads
ditag/five-dollar-genome-analysis-pipeline
Workflows used for WGS data processing -- replaced by https://github.com/gatk-workflows/gatk4-genome-processing-pipeline
ditag/FlashWeave.jl
Inference of microbial interaction networks from large-scale heterogeneous abundance data
ditag/GenomicRanges
Representation and manipulation of genomic intervals
ditag/hail
Scalable genomic data analysis.
ditag/I-Shell-Do-This
A growing repository of shell scripts to automate day-today activities of a NGS data analyst
ditag/karyoploteR
karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
ditag/KrakenTools
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
ditag/metapi
A general metagenomics data mining system focus on robust microbiome research
ditag/metaWRAP
MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
ditag/plotCoverageExons.py
Plot the coverage at some specific region from multiple bam files
ditag/prokka
:zap: :aquarius: Rapid prokaryotic genome annotation
ditag/q2-sidle
A QIIME 2 implementation of SMURF
ditag/seqtk
Toolkit for processing sequences in FASTA/Q formats
ditag/SGVFinder
ditag/shorah
Repo for the software suite ShoRAH (Short Reads Assembly into Haplotypes)
ditag/stringtie
Transcript assembly and quantification for RNA-Seq
ditag/vcfR
Tools to work with variant call format files
ditag/viralMetagenomicsPipeline
Pipeline for metagenomic community analysis using DNA isolated from virus-like particles
ditag/wastewater_sarscov2
A repository for sharing data, analyses, and results from Bay Area wastewater Sars-CoV-2 sequencing
ditag/webin-cli
Webin command line submission interface.