• Stars
    star
    2
  • Language
    Python
  • Created almost 3 years ago
  • Updated over 2 years ago

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

Instructions on how to convert Allen Brain Atlas data into AnnData files

More Repositories

1

pagoda2

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
JavaScript
203
star
2

conos

R package for the joint analysis of multiple single-cell RNA-seq datasets
R
191
star
3

numbat

Haplotype-aware CNV analysis from single-cell RNA-seq
R
161
star
4

Baysor

Bayesian Segmentation of Spatial Transcriptomics Data
Julia
144
star
5

dropEst

Pipeline for initial analysis of droplet-based single-cell RNA-seq data
C++
85
star
6

cacoa

Single-cell Case Control Analysis
R
46
star
7

scITD

Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
R
41
star
8

vrnmf

Volume-regularized NMF
R
17
star
9

hahmmr

Haplotype-aware Hidden Markov Models for detecting CNVs from bulk RNA-seq
R
13
star
10

sccore

Core utilities for single-cell RNA-seq
R
12
star
11

N2R

R extensions to N2 implementing approximate nearest neighbor search methods
C++
10
star
12

leidenAlg

Implements the Leiden algorithm via an R interface
C
9
star
13

NumbatAnalysis

Analysis scripts and notebooks for Numbat paper
R
7
star
14

gpsFISH

Optimization of gene panels for targeted spatial transcriptomics
R
6
star
15

cap-example

An example of proposed CAP annotation view
5
star
16

BaysorAnalysis

Analysis for the Baysor paper
Jupyter Notebook
5
star
17

scistreer

R/Rcpp implementation of the ScisTree algorithm
R
5
star
18

dropestr

Preprocessing of Droplet-based Single-Cell RNA-seq Data
R
4
star
19

cap-pipeline-config

Building ontology pipeline configurations for the Cell Annotation Platform
Python
3
star
20

cacoaAnalysis

Analysis for the Cacoa paper
R
2
star
21

conosViz

Shiny App to Visualize Dendrograms and Heatmaps from Conos
R
2
star
22

cap_ontology

An ODK based repo that allows us to finely tailor content for loading into the KB and also to manage content generated for CAP
Makefile
2
star
23

scLiTr

Repository for the scLiTr (single-cell Lineage Tracing analysis) python package
Python
2
star
24

conosPanel

Package with data used by conos: panel of four samples with 3000 cells each
R
1
star
25

drat

Drat repo with R packages
1
star
26

p2data

Package with data used by pagoda2, 3000 bone marrow cells
R
1
star
27

cap-pipeline-dumps

Python
1
star
28

simulatedNMF

Package with data used by vrnmf, simulated NMF matrices
R
1
star
29

cap_organ_slim

Makefile
1
star