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idemp

Barcode demultiplex for Illumina I1, R1, R2 fastq.gz files

idirect

igraph

Library for the analysis of networks

illumina-utils

A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).

imagegp

instrain

Bioinformatics program inStrain

interproscan

ipython

Official repository for IPython itself. Other repos in the IPython organization contain things like the website, documentation builds, etc.

irkernel

R kernel for Jupyter

iwanthue

Colors for data scientists.

jbrowse

A modern genome browser built with JavaScript and HTML5.

jgi-query

A simple command-line tool to download data from the Joint Genome Institute's database

keggcharter

A tool for representing genomic potential and transcriptomic expression into KEGG pathways

keggdecoder-binder

metabolic heatmap

kentutils

UCSC command line bioinformatic utilities

keras

Deep Learning for humans

khmer

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

kofam_scan

CLI tool to annotate genes with KOfam

kraken

Kraken taxonomic sequence classification system

kraken2

The second version of the Kraken taxonomic sequence classification system

kraken_db_install_scripts

Updated Kraken DB install scripts to cope with new-ish NCBI structure

krona

Interactively explore metagenomes and more from a web browser.

learn-python3

Learn Python 3 Sample Code

learnpythonthehardway

Learn Python The Hard Way course exercises

lifecyclemanuscript

Analyses for Plos Biology Rice Microbiome Manuscript

liu_side_projects_metagenome_genome

liupfskygre.github.io

mac-setup

:rocket: Automatically install, configure, and run the most popular programs of several stacks to work offline on a Mac and in clouds.

mag-isolate-comparison

reproducible rebuttal of Garg et al. preprint

make_silva_db

General procedure for making QIIME 2 compatible SILVA reference files