f6v

seqtk

Toolkit for processing sequences in FASTA/Q formats

bioicons

A library of free open source icons for science illustrations in biology and chemistry

hrbrthemes

:lock_with_ink_pen: Opinionated, typographic-centric ggplot2 themes and theme components

gganatogram

Create anatograms using ggplot2

hdWGCNA

High dimensional weighted gene co-expression network analysis

openproblems

Formalizing and benchmarking open problems in single-cell genomics

Single-nuclei-epigenomic-and-transcriptomic-landscape-in-Alzheimer-disease

Single-nuclei RNA-seq and ATAC-seq in Alzheimer's disease

ulcerative_colitis

CellFishing.jl

Fast and scalable cell search tool

umi-normalization

Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Genome Biology

immuneSIM

scDeepCluster_pytorch

Pytorch implementation of scDeepCluster for Single Cell RNA-seq data

igblast

Detailed explanation on how to setup database for NCBI IgBlast executable, and using it in Python

amp_phase1_ra

:ear_of_rice: Zhang, et al, Nature Immunology, 2019. Use single-cell transcriptomics and proteomics to study autoimmune diseases.

T-cell-effectorness

Codes used for all the data analysis steps in the paper "Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4+ T cells to cytokines"

RA_scRNA

Rheumatoid Arthritis project. single cell RNA sequencing data.

hWAT_singlecell

meta-analysis of new and published human WAT single cell data

baseline

Reproducible workflows for the data analysis of "Baseline" project

AutoCAT

CZI-Latent-Assessment

Supplement to the report in https://greenelab.github.io/czi-hca-report/

seurat-docker

Docker images of Seurat

parabiosis

Jupyter notebooks describing downstream computational analyses of "Molecular hallmarks of heterochronic parabiosis at single cell resolution"

SingleBCell-FluVaccine

Analysis of single-cell and repertoire sequencing for Horns et al. Cell Reports 2020

TCRpower

Power calculator for determining the minimum number of reads and sampled cells needed to detect a rare T-cell clonotype from receptor sequencing.

Marsh_et-al_2022_scRNAseq_Dissociation_Artifacts

Code to reproduce analysis objects for the data contained in Marsh et al., 2022

zero_types_paper

Code to reproduce analysis and figures in the Zero Types Paper

intel-mkl-docker

Docker image that has intel-mkl installed. Provides debian:buster and ubuntu:bionic based images on docker hub.

BD_project

CD8_aging_figure_scripts

Figure Scripts for the healthy CD8 Aging Manuscript

Temra-IL7R-Senescence

Pipeline used for the analysis