Discover Teichlab/spectrum-of-differentiation-supplements Open Source

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Mirror of analysis files for "Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells"

scg_lib_structs

Collections of library structure and sequence of popular single cell genomic methods

cellphonedb

celltypist

A tool for semi-automatic cell type classification

bbknn

SpatialDE

Test genes for Spatial Variation

Jupyter Notebook

143

tracer

TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data

Python

118

cellhint

A tool for semi-automatic cell type harmonization and integration

Python

MultiMAP

MultiMAP for integration of single cell multi-omics

Python

embl-single-cell-course-2016

Material for lecture at the EMBL Single Cell Course 2016

Jupyter Notebook

drug2cell

Gene group activity utility functions for Scanpy

Jupyter Notebook

bracer

BraCeR - reconstruction of B cell receptor sequences from single-cell RNAseq data

Python

cellity

Genes2Genes

Aligning gene expression trajectories of single-cell reference and query systems

Jupyter Notebook

Pan_fetal_immune

Collection of scripts for analysis of pan fetal immune atlas

sctk

celloline

GPfates

HCA_Heart_ver2

covid19_MS1

Analysis notebooks for "SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes".

Jupyter Notebook

visium_stitcher

Stitch multiple Visium slides together

Jupyter Notebook

limbcellatlas

This repository contains codes used for the human fetal limb cell atlas.

Jupyter Notebook

innate_evo

thymusatlas

Jupyter Notebook

celltypist_wiki

Materials and scripts for building cell type encyclopedia table

Python

KIRid

Shell

TissueImmuneCellAtlas

Jupyter Notebook

TissueTag

Python package to interactively annotate histological images within a jupyter notebook

Jupyter Notebook

readquant

Convenience package for parsing RNA-seq quantification results

Python

RCA

Residual Component Analysis

Jupyter Notebook

NaiveDE

The most trivial DE test based on likelihood ratio tests

Python

thymus_spatial_atlas

general repo that holds all analysis and figures for the thymus spatial atlas by Yayon, Kedlian, Boehme, Radtke and many more!

Jupyter Notebook

SpaceTimeGut

Analysis of scRNA-seq and V(D)J data of almost half a million cells from up to five anatomical regions in the developing and up to eleven distinct anatomical regions in healthy pediatric and adult human gut.

Jupyter Notebook

SKM_ageing_atlas

Jupyter Notebook

scrnatb

Single Cell RNA-Seq analysis toolbox for Python

Python

basespace_fq_downloader

A fastq downloader from basespace that actually works.

Python

basecloud

Base R/python/etc. internal OpenStack cloud setup for Teichlab

Shell

rbcde

Rank-biserial correlation coefficient for big data marker detection

Python

snp2cell

cell type specific, trait-associated gene regulation

Python

mapcloud

10X/SS2/spatial transcriptomics/genotyping internal cloud pipeline

Shell

cellphonedb-data

cell2tcr

Inference of TCR motifs

Jupyter Notebook

treg-gut-niches

Data pre-processing and analysis scripts for the article "Immune microniches shape intestinal Treg function"

Jupyter Notebook

COVID-19paed

power-analysis-material

Jupyter Notebook

iss_patcher

Approximate missing features from higher dimensionality data neighbours

Jupyter Notebook

covid19_oral

Jupyter Notebook

starters

Computational setup checklist for new starters

G2G_notebooks

Analysis notebooks for G2G MS

Jupyter Notebook

bbknn_preprint

Archival notebooks from the BBKNN preprint, removed from the paper

Jupyter Notebook

lung-immune-cell-atlas

This is a folder containing information of the human fetal lung leukocyte atlas

HTML

sctkr

A deposit of functions that perform common tasks for single cell analysis

Teichlab/spectrum-of-differentiation-supplements

Teichlab

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