334 Open source projects that are alternatives of or similar to souporcell

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

Spatial alignment of single cell transcriptomic data.

Collection of scripts for bacterial genomics

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Papers with code for single cell related papers

R package - Analysis of Single Cell Expression, Normalisation and Differential expression (ascend)

A tool for fast and accurate summarizing of variant calling format (VCF) files

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

Single cell type annotation guided by cell atlases, with freedom to be queer

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

Ultrafast sequence typing and gene detection from NGS raw reads

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.

Harmony framework for connecting scRNA-seq data from discrete time points

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

Interactive assembly and analysis of RAD-seq data sets

cTPnet Package

The Biochemical Algorithms Library

DeepChem 2017: Deep Learning & NLP for Computational Chemistry, Biology & Nano-materials

Single-cell Hierarchical Poisson Factorization

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data

An R framework for phylostratigraphy

An R Package for Geneset Enrichment Workflows

Multilocus sequence typing by blast using the schemes from PubMLST

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

Learn interpretable computational phenotyping models from k-merized genomic data

A package for designing activity-informed nucleic acid diagnostics for viruses.

🐳 Bio-dockers: dockerized bioinformatic tools

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

Robust and scalable inference of cell lineages from gene expression data.

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using coalescent and concatenation approaches

Command line utility for manipulating Illumina-generated FastQ files.

Grammar of Scalable Linked Interactive Nucleotide Graphics

Myokit: A simple interface to cardiac cellular electrophysiology

This is the main repository for the HackBio'2020 Virtual Internship Experience ❤️

A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.

Code and Data to accompany "Dilated Convolutions for Modeling Long-Distance Genomic Dependencies", presented at the ICML 2017 Workshop on Computational Biology

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

STAPLE (Shared Tools for Automatic Personalised Lower Extremity modelling) consists of a collection of methods for generating skeletal models from three-dimensional bone geometries, usually segmented from medical images. The methods are currently being expanded to create complete musculoskeletal models.

Tools for analyzing 10X Genomics data

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

Conversion between scRNA-seq objects

MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.

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

Numerical Encoding for Human Genetic Variants

mgatk: mitochondrial genome analysis toolkit

screenlamp is a Python toolkit for hypothesis-driven virtual screening

Identify phage regions in bacterial genomes for masking purposes

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

Predict AMPs in (meta)genomes and peptides

Spark VCF data source implementation for Dataframes

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

Predicting protein structure through sequence modeling

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

Resource of human chromosome schematics & images

WebAssembly modules for genomics

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

find large indels (in the blind spot between GATK/freebayes and SV callers)