128 Open source projects that are alternatives of or similar to kmer-homology-paper

R package to visualize gene expression data based on weighted kernel density estimation

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

Single-cell Orientation Tracing

mgatk: mitochondrial genome analysis toolkit

Tracking and proposing changes to SDL's public APIs.

Processing of single cell RNAseq data for the recovery of TCRs in python

PhyML -- Phylogenetic estimation using (Maximum) Likelihood

scLearn：Learning for single cell assignment

VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps

🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

Visualize the evolution of a file tracked by git

Differential expression analysis for single-cell RNA-seq data.

Редактируемая статья для блога: систематизация информации по симуляции эволюции

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

Multiome GRN inference.

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

An R implementation of the SINCERA pipeline for single cell RNA-seq profiling analysis

A collection of 50+ trajectory inference methods within a common interface 📥📤

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

Single-Cell Omics Preparation Entity Tools

CUT&RUN and CUT&Tag data processing and analysis

Write DB migrations with SQL and run them with a CLI

Single-cell exploratory data analysis for RNA-Seq

Tools for single-cell data processing

Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.

Metacell - Single-cell mRNA Analysis

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

spatial transcriptome, single cell

Supported highly optimized and flexible genetic algorithm package for python

Methods for detecting doublets in single-cell sequencing data

A tool for semi-automatic cell type annotation

Cutting Edge UI Components for Modern Developers

kallisto | bustools workflow for pre-processing single-cell RNA-seq data

Code for the empty droplet and cell detection project from the HCA Hackathon.

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

Spatial Single Cell Analysis in Python

Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)

R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...

Convert between AnnData and SingleCellExperiment

Graph-linked unified embedding for single-cell multi-omics data integration

R API and htmlwidget for Vitessce

Bead-based single-cell atac processing

Discrete Distributional Differential Expression

EXONA: The Evolutionary eXploration of Neural Networks Framework -- EXACT, EXALT and EXAMM

Citylines.co is a collaborative platform for mapping the transit systems of the world!

Efficient genotyping bi-allelic SNPs on single cells

No description or website provided.

Scripts to run and benchmark scRNA-seq cell cluster labeling methods

Evolution Simulation in XNA Refresh

Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)

De novo annotation of young retrotransposons

scisorseqr is an R-package for processing of single-cell long read data and analyzing differential isoform expression across any two conditions

Mouse cell atlas

Papers with code for single cell related papers

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

Single cell analysis in the browser

💡 💾 💽 A simple, intuitive and Efficient single cell binary Data Storage format