Awesome Open Source

Programming Languages

Search results for bioinformatics single cell

bioinformatics x

68 search results found

Awesome Single Cell ⭐ 2,784

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

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Single Cell Pseudotime ⭐ 367

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

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

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

R toolkit for the analysis of single-cell chromatin data

Octopus ⭐ 285

Bayesian haplotype-based mutation calling

DANCE: A Deep Learning Library and Benchmark Platform for Single-Cell Analysis

Immunarch ⭐ 256

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

Single cell perturbation prediction

Youtubetutorials ⭐ 180

R package for analyzing single-cell RNA-seq data

Omicverse ⭐ 159

A python library for multi omics included bulk and single cell RNA-seq analysis.

Single cell analysis in the browser

Decoupler Py ⭐ 112

Python package to perform enrichment analysis from omics data.

Tools for single-cell data processing

Cell_blast ⭐ 74

A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.

Singlecellhaystack ⭐ 68

Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

Rapids_singlecell ⭐ 66

Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.

Scatac Pro ⭐ 64

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

Single Cell Training ⭐ 63

SIB course on single cell transcriptomics by mostly using the Seurat pipeline

Cirrocumulus ⭐ 63

Bring your single-cell data to life

Cut Runtools 2.0 ⭐ 62

CUT&RUN and CUT&Tag data processing and analysis

Statistical approach for removing unwanted variation from multiple single-cell datasets

Spatial-Linked Alignment Tool

Cell2cell ⭐ 44

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

Identifying tumor cells at the single-cell level using machine learning

Spatialtranscriptomics ⭐ 34

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

Sscclust ⭐ 32

simpler single cell RNAseq data clustering

Cytometry Clustering Comparison ⭐ 30

R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data

Next-Gen Sequencing tools from the Horvath Lab

Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping

Csbb Shiny ⭐ 28

Computational Suite for Bioinformaticians and Biologists (CSBB) is a RShiny application developed with an intention to empower researchers from wet and dry lab to perform downstream Bioinformatics analysis

Gcmodeller ⭐ 27

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

Seuratv3wizard ⭐ 26

A web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat v3

ASAP : Automated Single-cell Analysis Pipeline

Beyondcell ⭐ 23

Beyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq data and proposing cancer-specific treatments.

Citefuse ⭐ 23

Cell2sentence Ft ⭐ 21

Cell2Sentence turns scRNA-seq data into text for LLM training.

Cshl Singlecell 2017 ⭐ 20

Single Cell Analysis course at Cold Spring Harbor Laboratory 2017

Schicexplorer ⭐ 19

Single-cell Hi-C data analysis toolbox

Crop Seq ⭐ 19

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

Netsmooth ⭐ 18

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

Muto_wilson_ncomm_2020 ⭐ 17

Workflow for analysis of healthy human kidney by snRNAseq and snATACseq

Splatter Paper ⭐ 15

Data and analysis for the Splatter paper

Omicssuite.github.io ⭐ 15

OmicsSuite website for releasing new version.

Uncurl_python ⭐ 14

UNCURL is a tool for single cell RNA-seq data analysis.

Bgeedb_r ⭐ 13

Source code of the R packge BgeeDB to use data from the Bgee database

Mdmcleaner ⭐ 13

MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs

Clustassess ⭐ 13

Tools for assessing clustering robustness

Genetic Heterogeneity Profiling by Single Cell RNA Sequencing

Rna Combine ⭐ 11

RNA-seq data comprehensive data analysis toolbox

NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization

An R package for analyzing high-dimensional cytometry data using the tidyverse.

Marcopolo ⭐ 9

MarcoPolo is a clustering-free approach to the exploration of bimodally expressed genes along with group information in single-cell RNA-seq data

Trisicell ⭐ 9

Scalable tumor phylogeny inference and validation from single-cell RNA or DNA data

A tool to quantify transposable elements expression in scRNA-seq

Singlecellhaystack Py ⭐ 8

Finding surprising needles (=features) in haystacks (=single cell/spatial genomics data).

Supervised cell type identification for scATAC-seq data

MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data

Single Cell Experiments ⭐ 7

Experiments to run single cell analyses efficiently at scale using Zarr, anndata, Scanpy, and Apache Spark

Single Cell RNA-seq UMI Filtering Facilitator

Accurately annotating scRNA-seq data using two rounds of reference-based classification

Single Cell Genomes with Allele Specificity

Dea_seurat ⭐ 6

A Snakemake workflow for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.

This is the repository which contains the code that was used to generate the results and figures of the “Single-cell RNA-sequencing reveals widespread personalized, context-specific gene expression regulation in immune cells” paper (https://www.biorxiv.org/content/10.1101/2021.06.0

This is a standalone interactive Shiny tool to analyze and explore single-cell RNA-seq data from human coronary artery.

Scphylo Tools ⭐ 5

a python toolkit for single-cell tumor phylogenetic analysis

Phd Thesis ⭐ 5

My PhD thesis - "Tools and techniques for single-cell RNA sequencing data"

Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data (Nature Communications, 2023)

Classification of Single cells by Transfer Learning

Related Searches

Python Bioinformatics (1,711)

Bioinformatics Genomics (541)

R Bioinformatics (490)

Bioinformatics Genome (444)

Jupyter Notebook Bioinformatics (320)

Pipeline Bioinformatics (283)

C Plus Plus Bioinformatics (261)

Bioinformatics Sequencing (250)

Bioinformatics Computational Biology (193)

Javascript Bioinformatics (184)

1-68 of 68 search results

Privacy | About | Terms | Follow Us On Twitter

Copyright 2018-2024 Awesome Open Source. All rights reserved.