80 Open source projects that are alternatives of or similar to Pando

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

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

Bead-based single-cell atac processing

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

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

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

Single-cell copy number calling and event history reconstruction.

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

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

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

R package to do the Ligand Receptor Analysis Visualization

Mouse cell atlas

Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders

Conditional out-of-distribution prediction

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

Next-Gen Sequencing tools from the Horvath Lab

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

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

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

Single-Cell Omics Preparation Entity Tools

Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.

An ontology of cell types

CUT&RUN and CUT&Tag data processing and analysis

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

scRNA-seq data visualization from scrattch

Digital Cell Sorter (DCS): single cell RNA-seq analysis toolkit. Documentation:

Convert between AnnData and SingleCellExperiment

A tool for semi-automatic cell type annotation

Single cell analysis in the browser

A tool to identify, orient, trim and rescue full length cDNA reads

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

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

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

A prediction model for differential gene expression (DE) based on genome-wide regulatory interactions

Workshop on tidytranscriptomics: Performing tidy transcriptomics analyses with tidybulk, tidyverse and tidyheatmap

Pipeline for annotating genomes using long read transcriptomics data with pinfish

Simulating single-cell data using gene regulatory networks 📠

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

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

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

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

R API and htmlwidget for Vitessce

Clone identification from single-cell data

Tools for single-cell data processing

Code pipeline for the PaccMann^RL in iScience: https://www.cell.com/iscience/fulltext/S2589-0042(21)00237-6

BACNET is a Java based platform to develop website for multi-omics analysis

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

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

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

Reference-based transcript discovery from long RNA read

Efficient genotyping bi-allelic SNPs on single cells

just annotate it, dammit!

MERlin is an extensible analysis pipeline applied to decoding MERFISH data

AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project

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

TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

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

Predicting regulatory DNA elements based on epigenomic signatures