83 Open source projects that are alternatives of or similar to immunarch

immuneML is a platform for machine learning analysis of adaptive immune receptor repertoire data.

Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data

The Read Origin Protocol (ROP) is a computational protocol that aims to discover the source of all reads, including those originating from repeat sequences, recombinant B and T cell receptors, and microbial communities.

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

An ultra-sensitive and precise tool for characterizing T cell CDR3 sequences in TCR-seq and RNA-seq data.

No description or website provided.

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

Simulating single-cell data using gene regulatory networks 📠

A data-centric flow/mass cytometry automated analysis framework

Mouse cell atlas

An interactive web portal for exploring immuno-oncology data

R package to do the Ligand Receptor Analysis Visualization

Comparison of dimensionality reduction methods

ImmuneDB - A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data

SHARP: Single-cell RNA-seq Hyper-fast and Accurate processing via ensemble Random Projection

A user friendly RabbitMQ library written in Golang.

Precision HLA typing from next-generation sequencing data

A Parity Substrate runtime implementation of a simple Token Curated Registry (TCR)

Conditional out-of-distribution prediction

BEER: Batch EffEct Remover for single-cell data

Bead-based single-cell atac processing

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

A react.js frontend for Substrate TCR runtime.

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

⚙️ Matching T-cell repertoire against a database of TCR antigen specificities

Dynamical systems methods for RNA velocity analysis

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

Tools for single-cell data processing

Clone identification from single-cell data

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

Convert between AnnData and SingleCellExperiment

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

CUT&RUN and CUT&Tag data processing and analysis

Next-Gen Sequencing tools from the Horvath Lab

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

Python Program To Send Instagram Story Views

Single cell analysis in the browser

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

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

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

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

Information and instructions for trying TCR workflow (test && commit || revert)

A tool for semi-automatic cell type annotation

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

Single-cell copy number calling and event history reconstruction.

Single-Cell Omics Preparation Entity Tools

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

<<------ Use SnapATAC!!

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

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

Reference mapping for single-cell genomics

Papers with code for single cell related papers

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.

IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data. Find full documentation at:

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

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

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

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

Efficient genotyping bi-allelic SNPs on single cells

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