amandabirmingham Goto Github PK

2018-10-11-ucsdccbb

c-view-currents

An extension to the C-VIEW (COVID-19 VIral Epidemiology Workflow) pipeline that uses Freyja to identify variants and lineages prevalent in mixed-input samples like wastewater.

custom_metadata_generators

fork_metagenomics_pooling_notebook

Jupyter notebooks to assist with sample processing

fork_mg-scripts_copy_sequences_branch

Knight Lab internal Metagenomic processing scripts for demultiplexing, QC and host removal

fork_qiime2

Official repository for the QIIME 2 framework.

fork_qp-knight-lab-processing

inspectseq_metadata_validator

Tools to validate InspectSeq metadata files for use in C-VIEW

labman

lab manager for plate maps and sequence flows

mali-dual-crispr-pipeline

This repository contains code for the dual-CRISPR screen analysis pipeline developed to analyze results from the dual-CRISPR screening system set up by the labs of Dr. Prashant Mali and Dr. Trey Ideker. The software is developed by Amanda Birmingham and Roman Sasik of the Center for Computational Biology and Bioinformatics at the University of Cal

mopp

Multi-Omics Processing Pipeline (MOPP)

pysyndna

Python implementation and extension of SynDNA ("a Synthetic DNA Spike-in Method for Absolute Quantification of Shotgun Metagenomic Sequencing", Zaramela et al., mSystems 2022

q2-diversity

q2-pysyndna

QIIME 2 plugin for pysyndna functionality

q2-surpi

q2cwl-fork

Prototype interface for automatically generating CWL tools from QIIME 2 actions

q2templater

Generate Galaxy tool descriptions automatically from QIIME 2 actions.

qadabra-fork

Snakemake workflow for comparison of differential abundance ranks

qiimp

Web application to collect metadata specifications from an experimenter and produce metadata input files with appropriate constraints

qiimp2

qiita

Qiita - A multi-omics databasing effort

sars-cov-2_wastewater_san-diego