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Jack Sumner (jtsumner)

jtsumner

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lab-manuscript-template

An academic manuscript template with writing tips in both LaTeX and MS Word format generated by the Capra Lab (2/2022)

Language:TeXLicense:MITStargazers:19Issues:0Issues:0

bioRxiv-word-template

MS Word template for styling a manuscript for a bioRxiv submission

License:GPL-3.0Stargazers:31Issues:0Issues:0

ggstar

:star: star layer for ggplot2

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gt

Easily generate information-rich, publication-quality tables from R

Language:RLicense:NOASSERTIONStargazers:2013Issues:0Issues:0

msamtools

Metagenomics-related extended functionalities to samtools

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igv-reports

Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.

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ggtrace

ggplot2 geoms to outline groups of data points

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ghibli

Studio Ghibli colour palettes

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bayesplot

bayesplot R package for plotting Bayesian models

Language:RLicense:GPL-3.0Stargazers:431Issues:0Issues:0

tsfresh

Automatic extraction of relevant features from time series:

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metadeconfoundR

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Rhea

A set of R scripts for the analysis of microbial profiles

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r-color-palettes

Comprehensive list of color palettes available in R ❤️🧡💛💚💙💜

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knitr-examples

A collection of knitr examples

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COPD_multiomics

This repository contains computer codes for main analyses of the manuscript titled 'Multi-omic Landscape of Airway Microbe-Host Interaction in Chronic Obstructive Pulmonary Disease'.

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pavian

🌈 Interactive analysis of metagenomics data

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KrakenTools

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

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getting-started-with-genomics-tools-and-resources

Unix, R and python tools for genomics and data science

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genomicspapers

The Leek group guide to genomics papers

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gencore

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

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snakemake_assemble

Modular snakemake workflow for assembly-based metagenomics

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sunbeam

A robust, extensible metagenomics pipeline

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FastANI

Fast Whole-Genome Similarity (ANI) Estimation

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emmeans

Estimated marginal means

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snakefmt

The uncompromising Snakemake code formatter

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wgsim

Reads simulator

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SqueezeMeta

A complete pipeline for metagenomic analysis

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MicrobiomeBestPracticeReview

Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing

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nonpareil

Estimate metagenomic coverage and sequence diversity

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metagMisc

Miscellaneous functions for metagenomic analysis.

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