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2020-advanced_single_cell_rna_seq

Building on material from Introduction to Single Cell RNA-Seq, this workshop aims to cover advanced topics, including TCR and trajectory analysis. Instruction in introductory analysis will not be provided.

2020_grant

Code base for the Grant, Morales-Nebreda, and Markov et al., “Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia” Nature (2021) paper

2020_wilk_covid

Reproducibility repository accompanying Wilk, Rustagi, Zhao, et al. "A single-cell atlas of the peripheral immune response to severe COVID-19"

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

biocycapi

R package providing BioCyc API.

bioinformatics_pipeline

Bioinformatics Pipeline

copd_metaanalysis

This depository contains key scripts used to analyze the data in the manuscript "Multi-omic meta-analysis identifies functional signatures of airway microbiome in COPD" by Wang et al.

covid-19-blood-bulk-rna-seq

all script and necessary resources to reproduce the figures

covid-19paed

covid19-autopsy

covid_scmultiome

Reproducibility repository accompanying Wilk, Lee, Wei, Parks, et al. "Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19" bioRxiv (2020).

covidomics

Longitudinal multi-omics analysis identifies responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories

covidpbmc

Multi-omics profiling of peripheral immune system response to SARS-CoV-2 infection

cuimc-nyp_covid_autopsy_lung

dl-mo

The deeplearning methods for multi-omics data fusion

flowcytometryscripts

forall

genomic_surveillance_of_imported_covid-19_guangzhou

hackathon

Multi-omics studies are available here

idm-activation-script

IDM Activation & Trail Reset Script

immune-dynamics-during-ad5-ncov-immunization-

its2-pipeline

keggapi

R package providing KEGG API.

lcmv-code-2022

Code for Daniel*, Yost*, Hsiung*, et al. Divergent clonal differentiation trajectories of T cell exhaustion (2022).

mba

Monkey brain atlas

metagenome

Metagenome analysis pipeline

mis-c_scrnaseq

mouse-xx-xy-c1

mouse_embryo

Graphviz graphs using edge data from String-db

mycobiome

Pan-cancer mycobiome atlas