Pinned Repositories
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_qiime2
Official repository for the QIIME 2 framework.
inspectseq_metadata_validator
Tools to validate InspectSeq metadata files for use in C-VIEW
labman
lab manager for plate maps and sequence flows
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-pysyndna
QIIME 2 plugin for pysyndna functionality
qiimp2
AmandaBirmingham's Repositories
AmandaBirmingham/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.
AmandaBirmingham/2018-10-11-ucsdccbb
AmandaBirmingham/custom_metadata_generators
AmandaBirmingham/fork_metagenomics_pooling_notebook
Jupyter notebooks to assist with sample processing
AmandaBirmingham/fork_qiime2
Official repository for the QIIME 2 framework.
AmandaBirmingham/inspectseq_metadata_validator
Tools to validate InspectSeq metadata files for use in C-VIEW
AmandaBirmingham/labman
lab manager for plate maps and sequence flows
AmandaBirmingham/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
AmandaBirmingham/q2-pysyndna
QIIME 2 plugin for pysyndna functionality
AmandaBirmingham/q2-surpi
AmandaBirmingham/qiimp2
AmandaBirmingham/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
AmandaBirmingham/mopp
Multi-Omics Processing Pipeline (MOPP)
AmandaBirmingham/q2-diversity
AmandaBirmingham/q2cwl-fork
Prototype interface for automatically generating CWL tools from QIIME 2 actions
AmandaBirmingham/q2templater
Generate Galaxy tool descriptions automatically from QIIME 2 actions.
AmandaBirmingham/qadabra-fork
Snakemake workflow for comparison of differential abundance ranks
AmandaBirmingham/qiimp
Web application to collect metadata specifications from an experimenter and produce metadata input files with appropriate constraints
AmandaBirmingham/qiita
Qiita - A multi-omics databasing effort
AmandaBirmingham/SARS-CoV-2_WasteWater_San-Diego