62 Open source projects that are alternatives of or similar to crop-seq

Synthego ICE - Inference of CRISPR Editing software

CCTyper: Automatic detection and subtyping of CRISPR-Cas operons

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

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

Reference mapping for single-cell genomics

Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products

Convert between AnnData and SingleCellExperiment

Inference of switch-like differential expression along single-cell trajectories

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

Papers with code for single cell related papers

Single-cell copy number calling and event history reconstruction.

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

Software for exploration of gene expression data from single-cell RNA sequencing.

Tools for single-cell data processing

Clone identification from single-cell data

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

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

Single cell analysis in the browser

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

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

A fast, accurate, and modularized dimensionality reduction approach based on diffusion harmonics and graph layouts. Escalates to millions of samples on a personal laptop. Adds high-dimensional big data intrinsic structure to your clustering and data visualization workflow.

Conditional out-of-distribution prediction

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

Bead-based single-cell atac processing

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

Simulating single-cell data using gene regulatory networks 📠

Methods for detecting doublets in single-cell sequencing data

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data

Efficient genotyping bi-allelic SNPs on single cells

R package to do the Ligand Receptor Analysis Visualization

A tool for semi-automatic cell type annotation

SpacePHARER CRISPR Spacer Phage-Host pAiRs findER

mgatk: mitochondrial genome analysis toolkit

Non-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)

Experimental design framework for scRNAseq population studies (eQTL and DE)

Mouse cell atlas

Dynamical systems methods for RNA velocity analysis

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

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

The CRISPR assembler

Deep learning model for single-cell inference of multi-omic profiles from a single input modality.

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files

Manuscript for functional prediction of transcriptomic “dark matter” across species

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

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

A tool that allows to get UMI counts from a single cell protein assay

No description or website provided.

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

spatial transcriptome, single cell

Next-Gen Sequencing tools from the Horvath Lab

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

Single-Cell Omics Preparation Entity Tools

A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches

R API and htmlwidget for Vitessce

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

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

CUT&RUN and CUT&Tag data processing and analysis

Fast visualization tool for large-scale and high dimensional single-cell data