Stars
Decoding the functional networks of non-model organisms
A genome browser designed for complex structural variants and long reads.
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.
This is the alpha version of the CellOracle package
Software package for assigning SARS-CoV-2 genome sequences to global lineages.
Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.
Stain normalization tools for histological analysis and computational pathology
The repository provides code for running inference with the SegmentAnything Model (SAM), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.
Processing pipeline for pan-genome visulization and exploration
Uses deep learning to classify types of white blood cells in cell images from blood smear slides to aid in AML diagnosis.
Flexible Genotyping of Polyploids using Next Generation Sequencing Data
Suite of command-line tools to expedite analysis of exome variant data from multiple patients and multiple variant callers.
scripts and notebooks from sanbomics
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
A guide to using a Seurat object in conjunction with RNA Velocity
TRAjectory-based Differential Expression analysis for SEQuencing data
Individual level Differential Expression Analysis for Single cells
Haplotype-aware CNV analysis from single-cell RNA-seq
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Python library for calculting synergy of drug combinations using several drug synergy frameworks
Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics