ddiez / singleCellHaystack-py
Finding surprising needles (=features) in haystacks (=single cell/spatial genomics data).
☆11Updated 10 months ago
Related projects ⓘ
Alternatives and complementary repositories for singleCellHaystack-py
- RNA-velocity informed embeddings for visualizing cellular trajectories☆43Updated 2 years ago
- An R package performing object conversion from ArchRProject (ArchR) to Signac SeuratObject (Signac)☆32Updated 2 months ago
- Aligning gene expression trajectories of single-cell reference and query systems☆44Updated last month
- Updated scripts and pipelines for processing GESTALT data at single-cell resolution☆19Updated 3 years ago
- Multi-resolution Variational Inference☆22Updated last month
- R package for analysing single cell data☆48Updated last year
- Implements *CellAnnotator (aka *CAT/starCAT), annotating scRNA-Seq with predefined gene expression programs☆18Updated 2 weeks ago
- .h5mu files interface for Seurat☆26Updated 11 months ago
- Identify major cellular signals in bulk transcriptomes☆11Updated 2 years ago
- Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity☆19Updated 3 months ago
- Python library for plotting Cellphonedb results. Ported from ktplots R package.☆46Updated last month
- R/Bioconductor package for working with 10x scATACseq data☆38Updated last year
- ☆29Updated last year
- ☆61Updated last month
- Discover differential transcript usage from polyA-captured single cell RNA-seq data☆49Updated last year
- Toolkit for metacell analysis☆13Updated 3 months ago
- An R package for performing cell typing in SMI and other single cell data☆29Updated 2 months ago
- Calculate cluster similarity between clusters from different single cell datasets/batches/samples.☆16Updated 4 months ago
- AnnData interoperability in R☆58Updated this week
- Interactive visualisation of CellphoneDB results☆9Updated this week
- a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.☆49Updated last week
- Individual level Differential Expression Analysis for Single cells☆22Updated last year
- scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics☆50Updated 2 months ago
- Gene regulatory network containing signed transcription factor-target gene interactions☆61Updated 6 months ago
- R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data☆23Updated 5 months ago
- Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…☆45Updated 3 weeks ago
- Snakefile-based process to turn 1.4 million ocular cells into a unified meta-atlas☆24Updated 10 months ago
- psupertime is pseudotime ordering for single cell RNA-seq data with sequential labels☆38Updated 2 years ago
- Analysis cell-type-specific functional gene network, with SCINET and HumanNetv3☆38Updated 8 months ago
- Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.☆30Updated last month