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2018_bacon_charnock-jones

scRNA-Seq Analysis Scripts to accompany: Bacon, W.A., Hamilton, R.S., Yu, Z., Kieckbusch, J., Hawkes, D., Krzak, A., Abell, C., Colucci, F. & Charnock-Jones, D.S. (2018) Single-Cell Analysis Identifies Thymic Maturation Delay in Growth-Restricted Neonatal Mice

anndata

Annotated multivariate observation data

cfit

Common Factor Integration & Transfer learning (cFIT) for single cell RNA-seq data

docker-alpine

Dockerfile and other source files to build my alpine image

docker-ubuntu

Dockerfile and other source files to build my ubuntu image

dockerlabs

Docker - Beginners | Intermediate | Advanced

doubletdecon

A tool for removing doublets from single-cell RNA-seq data

doubletdeconseurat

Wrappers of DoubletDecon package

drop-seq-docker

Pipeline of Drop-seq tools with docker

fateid

R package for the inference of cell fate bias from single-cell RNA-seq data.

heca

Human embryonic cell altas

linux-vm-tools

Hyper-V Linux Guest VM Enhancements

mouse_embryonic_mirnas

The miRNA-mRNA analysis during mouse embryonic development

mycolors

An R package to generate diverse palette.

mydockerfiles

Dockerfiles and codes used to build my advanced docker images

myseuratwrappers

My extensions for Seurat package

mysingularity

Singularity def files and codes used to build my containers

python_for_data_analysis_2nd_chinese_version

《利用Python进行数据分析·第2版》

rapids-single-cell-examples

Examples of single-cell genomic analysis accelerated with RAPIDS

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

sccaf

Single-Cell Clustering Assessment Framework

scrublet

Detect doublets in single-cell RNA-seq data

sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression

seurat

R toolkit for single cell genomics

seurat-data

Dataset distribution for Seurat

seurat-disk

Interfaces for HDF5-based Single Cell File Formats

seurat-wrappers

Community-provided extensions to Seurat

seurat_reproducible

Explore the reproducibility of Seurat pipeline

thymusatlas

thymusatlasanalysis

Analysis for our 2018 Immunity paper (cell atlas of mouse thymus development).