kharchenkolab/cap_organ_slim

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kharchenkolab/cap_organ_slim

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pagoda2

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

conos

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

numbat

Haplotype-aware CNV analysis from single-cell RNA-seq

Baysor

Bayesian Segmentation of Spatial Transcriptomics Data

dropEst

Pipeline for initial analysis of droplet-based single-cell RNA-seq data

cacoa

Single-cell Case Control Analysis

scITD

Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition

vrnmf

Volume-regularized NMF

hahmmr

Haplotype-aware Hidden Markov Models for detecting CNVs from bulk RNA-seq

sccore

Core utilities for single-cell RNA-seq

N2R

R extensions to N2 implementing approximate nearest neighbor search methods

leidenAlg

Implements the Leiden algorithm via an R interface

NumbatAnalysis

Analysis scripts and notebooks for Numbat paper

gpsFISH

Optimization of gene panels for targeted spatial transcriptomics

cap-example

An example of proposed CAP annotation view

BaysorAnalysis

Analysis for the Baysor paper

Jupyter Notebook

scistreer

R/Rcpp implementation of the ScisTree algorithm

dropestr

Preprocessing of Droplet-based Single-Cell RNA-seq Data

cap-pipeline-config

Building ontology pipeline configurations for the Cell Annotation Platform

AllenBrain_AnnData

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

cacoaAnalysis

Analysis for the Cacoa paper

conosViz

Shiny App to Visualize Dendrograms and Heatmaps from Conos

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

scLiTr

Repository for the scLiTr (single-cell Lineage Tracing analysis) python package

conosPanel

Package with data used by conos: panel of four samples with 3000 cells each

drat

Drat repo with R packages

p2data

Package with data used by pagoda2, 3000 bone marrow cells

cap-pipeline-dumps

simulatedNMF

Package with data used by vrnmf, simulated NMF matrices