katrinakalantar Goto Github PK

abatelab

work done in the Abate Lab at UCSF to investigate microbial relationships in single-cell microbial genome sequencing data from environmental samples

adage-server

Webserver for ADAGE models.

amr-benchmark

Scripts to support AMR tool benchmarking study

amr-beta-support-scripts

Scripts to support analysis of CZ ID AMR beta module

applytybaltvae

Modified scripts to apply the Greene Lab Tybalt VAE to Host and Microbe mNGS data

cend-de-demo

demonstration of differential expression analysis using DESeq2

clustered-phylotree

WDL workflow for split-kmer phylogeny with pre-filtering by hierarchical clustering

cs267_hw2

Parallel particle simulation

czid-amr-heatmap

Prototype code for creating CZID-esque heatmap using AMR pipeline data

czid-ont-heatmap

Prototype code for creating CZID-esque heatmap using ONT pipeline

czid-prototype-ont-pipeline

Prototyping an ont-compatible metagenomic pipeline for czid

dropseqdb

Tools for visualization and analysis of single cell RNA-seq data, developed during my Spring Rotation in the DeRisi Lab at UCSF

earli-classifier

generative-experiments

early experimentation with generative art

idseq-benchmark-manuscript

Analyses presented in the manuscript: IDseq – An Open Source Cloud-based Pipeline and Analysis Service for Metagenomic Pathogen Detection and Monitoring

latex-moderncv

My latex resume using the moderncv template

mbalvta_comparison

metahostlab

minimal

Personal blog theme powered by Hugo

mngsdiversity

Basic Scripts for diversity analysis of mNGS data in DeRisi pipeline.

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

ncbi-compress-experiments

Experimenting with NCBI database compression for mNGS applications

nmlhc

Noisy Metagenomically Labelled Host Classifier

pathomodel

phagedisplaylib

prototype-nt-trie

Tools for accessing the NCBI database using marisa trie

rbm_basic

basic implementation of rules-based-model for pathogen identification from mNGS data

read-level-viz-experiment

runvadrwdl

wdl to run vadr module