Stars
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
Structural variation and indel detection by local assembly
Tools to process and analyze deep sequencing data.
This is the alpha version of the CellOracle package
Haplotype-aware CNV analysis from single-cell RNA-seq
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtool…
An easy-to-use Hi-C data processing software supporting distributed computation.
⚡ A Fast, Extensible Progress Bar for Python and CLI
Identify spatially variable genes by projecting to morphologically relevant curves
Codes for 'Hi-C profiling in tissues reveals tumour-specific three-dimensional chromatin domains and novel looping-mediated biological pathways in breast cancer endocrine resistance'
Fit Gamma-Poisson Generalized Linear Models Reliably
K-nearest neighbor smoothing for high-throughput single-cell RNA-Seq data
Extract 3D contacts (.pairs) from sequencing alignments
Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.
This is for enar datafest 2025, team #11 - Weiran Yang,Xinyang Fei, Junlu Wang
In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes
Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
Pipeline for calling mCAs and LoY with WGS data from the TOPMed project
Implement a ChatGPT-like LLM in PyTorch from scratch, step by step