nickp60

Trying to figure those "bacteria" things that people keep talking about

Pinned Repositories

annofilt
Filter Prokka assemblies for pangenome analysis
Language:Python3 2 11
cgfind
Minimal way to find and download complete prokaryotic genomes
Language:HTML2 2 01
EzClermont
Phylotype your strains using Clermont's 2013 method: ezclermont.org
Language:Python9 3 53
fcid
Language:Python14 1 11
happie
Horizontally Aquired Partial Pangenome of Inserted Elements
Language:Python6 4 00
plentyofbugs
Find your sequenced isolate an compatable reference genome based on location, interests, and average nucleotide identity
Language:Python2 2 01
ProphET
Language:Perl3 2 00
riboSeed
pipeline for using ribosomal flanking regions to improve bacterial genome assembly
Language:Python8 8 112
sraFind
Get SRA accessions from nucleotide accessions, assuming the authors did the right thing and made the data available
Language:R7 4 02

nickp60's Repositories

nickp60/fcid
Language:Python14 1 11
nickp60/EzClermont
Phylotype your strains using Clermont's 2013 method: ezclermont.org
Language:Python9 3 53
nickp60/rgi
Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
Language:Python1 0 0
nickp60/anadama2
AnADAMA2 is the next generation of AnADAMA (Another Automated Data Analysis Management Application). AnADAMA is a tool to capture your workflow and execute it efficiently on your local machine or in a grid compute environment (ie. sun grid engine or slurm).
Language:Python0 01
nickp60/boxr
:package: A high-level R interface for the box.com API
Language:R0 0
nickp60/Comparison_of_DA_microbiome_methods
Language:R0 0
nickp60/dada2
Accurate sample inference from amplicon data with single nucleotide resolution
Language:R1 0
nickp60/getupandrunning
Dear Future Me; this is to help get your system back to normal after Current You does something foolish.
Language:Shell2 0
nickp60/hecatomb
hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
Language:Python0 0
nickp60/humann
HUMAnN 3.0 is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).
Language:Python0 0
nickp60/isabl_cli
🤖 isabl Command Line Client and SDK.
Language:Python0 0
nickp60/jenkspy-feedstock
A conda-smithy repository for jenkspy.
0 0
nickp60/KrakenTools
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
Language:Python0 0
nickp60/metaerg
fork for fixing issue #12 and #36
Language:Perl0 0
nickp60/MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
Language:Python0 0
nickp60/micom
Python package to study microbial communities using metabolic modeling.
Language:Python0 0
nickp60/microclass
R package for microbial taxonomic classification
Language:R0 0
nickp60/mkdocs
Project documentation with Markdown.
nickp60/mkdocs-sample
A sample documentation site generated from Markdown.
0 0
nickp60/phanta
Language:Python0 0
nickp60/shiny-phyloseq
An interactive web application for demonstrating and using phyloseq.
Language:HTML0 0
nickp60/shunPykeR
Language:Jupyter Notebook0 0
nickp60/snakedeploy-issue
Language:Python0 0
nickp60/snakemake-container-inheiritance
Language:Python1 0
nickp60/snakemake-executor-plugin-lsf
LSF profile for Snakemake >= v8
1 0
nickp60/snakemake-singularity-issue
Language:Python1 0
nickp60/spectra
Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
Language:Jupyter Notebook0 0
nickp60/sytycs
So you think you can species?
Language:UnrealScript1 0
nickp60/taxumap
Language:Python
nickp60/whvr
Lazy shiny app for aligning 16S primers or amplicons to the cannonical reference
Language:R