Teichmann Group (@Teichlab)

Top repositories

1

scg_lib_structs

Collections of library structure and sequence of popular single cell genomic methods
HTML
413
star
2

cellphonedb

Python
342
star
3

celltypist

A tool for semi-automatic cell type classification
Python
225
star
4

bbknn

Batch balanced KNN
Python
147
star
5

SpatialDE

Test genes for Spatial Variation
Jupyter Notebook
143
star
6

tracer

TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
Python
118
star
7

cellhint

A tool for semi-automatic cell type harmonization and integration
Python
68
star
8

MultiMAP

MultiMAP for integration of single cell multi-omics
Python
51
star
9

embl-single-cell-course-2016

Material for lecture at the EMBL Single Cell Course 2016
Jupyter Notebook
44
star
10

drug2cell

Gene group activity utility functions for Scanpy
Jupyter Notebook
36
star
11

bracer

BraCeR - reconstruction of B cell receptor sequences from single-cell RNAseq data
Python
35
star
12

cellity

R
34
star
13

Genes2Genes

Aligning gene expression trajectories of single-cell reference and query systems
Jupyter Notebook
34
star
14

Pan_fetal_immune

Collection of scripts for analysis of pan fetal immune atlas
Jupyter Notebook
25
star
15

sctk

Python
21
star
16

celloline

Python
19
star
17

GPfates

Python
19
star
18

HCA_Heart_ver2

Jupyter Notebook
17
star
19

covid19_MS1

Analysis notebooks for "SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes".
Jupyter Notebook
13
star
20

visium_stitcher

Stitch multiple Visium slides together
Jupyter Notebook
13
star
21

limbcellatlas

This repository contains codes used for the human fetal limb cell atlas.
Jupyter Notebook
12
star
22

innate_evo

R
12
star
23

thymusatlas

Jupyter Notebook
11
star
24

celltypist_wiki

Materials and scripts for building cell type encyclopedia table
Python
10
star
25

KIRid

Shell
9
star
26

TissueImmuneCellAtlas

Jupyter Notebook
9
star
27

TissueTag

Python package to interactively annotate histological images within a jupyter notebook
Jupyter Notebook
8
star
28

readquant

Convenience package for parsing RNA-seq quantification results
Python
8
star
29

RCA

Residual Component Analysis
Jupyter Notebook
8
star
30

spectrum-of-differentiation-supplements

Mirror of analysis files for "Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells"
Jupyter Notebook
7
star
31

NaiveDE

The most trivial DE test based on likelihood ratio tests
Python
6
star
32

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
5
star
33

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
5
star
34

SKM_ageing_atlas

Jupyter Notebook
4
star
35

scrnatb

Single Cell RNA-Seq analysis toolbox for Python
Python
4
star
36

basespace_fq_downloader

A fastq downloader from basespace that actually works.
Python
4
star
37

basecloud

Base R/python/etc. internal OpenStack cloud setup for Teichlab
Shell
4
star
38

rbcde

Rank-biserial correlation coefficient for big data marker detection
Python
4
star
39

snp2cell

cell type specific, trait-associated gene regulation
Python
4
star
40

mapcloud

10X/SS2/spatial transcriptomics/genotyping internal cloud pipeline
Shell
3
star
41

cellphonedb-data

3
star
42

cell2tcr

Inference of TCR motifs
Jupyter Notebook
3
star
43

treg-gut-niches

Data pre-processing and analysis scripts for the article "Immune microniches shape intestinal Treg function"
Jupyter Notebook
3
star
44

COVID-19paed

R
2
star
45

power-analysis-material

Jupyter Notebook
2
star
46

iss_patcher

Approximate missing features from higher dimensionality data neighbours
Jupyter Notebook
2
star
47

covid19_oral

Jupyter Notebook
2
star
48

starters

Computational setup checklist for new starters
2
star
49

G2G_notebooks

Analysis notebooks for G2G MS
Jupyter Notebook
1
star
50

bbknn_preprint

Archival notebooks from the BBKNN preprint, removed from the paper
Jupyter Notebook
1
star
51

lung-immune-cell-atlas

This is a folder containing information of the human fetal lung leukocyte atlas
HTML
1
star
52

sctkr

A deposit of functions that perform common tasks for single cell analysis
R
1
star