patriciatran

patriciatran's Stars

• alshedivat/al-folio

  A beautiful, simple, clean, and responsive Jekyll theme for academics

  Language:HTML10.7k2455011k

• DerrickWood/kraken2

  The second version of the Kraken taxonomic sequence classification system

  Language:C++71429827271

• rrwick/Bandage

  a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

  Language:C++5813710996

• rrwick/Unicycler

  hybrid assembly pipeline for bacterial genomes

  Language:C++55330328131

• Ecogenomics/GTDBTk

  GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

  Language:Python4682345382

• bxlab/metaWRAP

  MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

  Language:Shell39117542191

• rrwick/Trycycler

  A tool for generating consensus long-read assemblies for bacterial genomes

  Language:Python305157628

• rrwick/Filtlong

  quality filtering tool for long reads

  Language:C++280143828

• biobakery/biobakery

  bioBakery tools for meta'omic profiling

  Language:Shell257164773

• wwood/kingfisher-download

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

  Language:Python24273437

• nf-core/mag

  Assembly and binning of metagenomes

  Language:Nextflow209154279106

• AnantharamanLab/METABOLIC

  A scalable high-throughput metabolic and biogeochemical functional trait profiler

  Language:Perl173418143

• biobakery/humann

  HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).

  Language:Python165144158

• tseemann/any2fasta

  Convert various sequence formats to FASTA

  Language:Perl12752417

• Russel88/CRISPRCasTyper

  CCTyper: Automatic detection and subtyping of CRISPR-Cas operons

  Language:Python8935316

• biocore/empress

  A fast and scalable phylogenetic tree viewer for microbiome data analysis

  Language:JavaScript451633331

• aemon-j/LakeEnsemblR

  An R package that facilitates multi-model ensembles for lake thermodynamics. Also includes tools for calibration, sensitivity analysis and data visualization.

  Language:HTML32106519

• opensciencegrid/cvmfs-singularity-sync

  Scripts to synchronize Singularity images to a CVMFS repository.

  Language:Python242212142

• SimonTopp/HackingLimnoWorkshop

  This repository contains a simple remote sensing modeling pipeline for predicting simple water quality parameters in lakes.

  Language:JavaScript162017

• aemon-j/LakeEnsemblR.WQ

  R Package to facilitate running ensembles of water quality models

  Language:R9109

• hdugan/NTLlakeloads

  Interpolate depth-discrete water quality data from NTL-LTER

  Language:R5201

• mrumi/MetaCompare2.0

  Language:Python5

• McMahonLab/FEET

  Finding Extracellular Electron Transfer proteins using FeGenie, HMMs, and cytochrome motifs.

  Language:Python40

• patriciatran/MAG_pipeline

  🐍 🧬 Turning my metagenomic MAG (metagenome-assembled genome) pipeline into a snakemake pipeline for increased reproducibility and scalability.

  Language:Python3100

• patriciatran/LakeMendota-PairedOmics

  R code used to clean, process, merge, and visualize data related to one of my thesis chapters.

  Language:R20

• patriciatran/LakeTanganyika

  Code to generate figures/analyses for the Lake Tanganyika project.

  Language:R2200

• patriciatran/dsos-aemon-j-2021

  Test website

  1100

• patriciatran/LakeEnsemblR_WQ

  R Package to facilitate running ensembles of water quality models

  1000

• patriciatran/MicrobialEcologyWorkshop

  Files, instructions and presentation during a presentation and workshop we gave on microbial ecology during the Annual Fall Workshops in Limnology at the Interuniversity Research Group for Limnology Research (GRIL) - EcoLac.

  1101

• patriciatran/Nitrogen_Project

  Project on under-ice Nitrogen cycling in Lake Mendota, during my internship at UW-Madison in the McMahon Lab during Spring 2018.

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