108 Open source projects that are alternatives of or similar to kallistobustools

A guide to using a Seurat object in conjunction with RNA Velocity

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.

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

Single cell analysis in the browser

Next-Gen Sequencing tools from the Horvath Lab

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

Dynamical systems methods for RNA velocity analysis

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

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

Fast in-silico normalization algorithm for NGS data

A versatile sequenced read processor for nanopore direct RNA sequencing

Fast and accurate gene fusion detection from RNA-Seq data

A proof of concept RNA-Seq pipeline with Nextflow

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

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

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

R package to do the Ligand Receptor Analysis Visualization

Mouse cell atlas

CellNet: network biology applied to stem cell engineering

RNASeq pipeline

Differential Gene Correlation Analysis

Single-Cell Omics Preparation Entity Tools

An automated RNA-seq pipeline using Nextflow

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

🚦 Run Picard on BAM files and collate 90 metrics into one file.

Single-cell copy number calling and event history reconstruction.

Create a cromphensive report of DEG list coming from any analysis of RNAseq data

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

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

CoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.

Simulating single-cell data using gene regulatory networks 📠

Scripts to import your FeatureCounts output into DEXSeq

Processing of single cell RNAseq data for the recovery of TCRs in python

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

Convert between AnnData and SingleCellExperiment

Clone identification from single-cell data

Bead-based single-cell atac processing

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

Feature extraction algorithm for genomic data

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Efficient genotyping bi-allelic SNPs on single cells

Multi-omics analysis protocols by Lyu.

Software for measuring poly(A) tail length and 3′-end modifications using a high-throughput sequencer

📊 Graphical User Interface for TCC package

Version 2.1.0 released

CUT&RUN and CUT&Tag data processing and analysis

Streamlining SLAM-seq analysis with ultra-high sensitivity

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

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

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

Conditional out-of-distribution prediction

Tools for single-cell data processing

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

Deep Learning based cell composition analysis with Scaden.

FEELnc : FlExible Extraction of LncRNA

CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.

A course on Analysing Next Generation (/High Throughput etc..) Sequencing data using Bioconductor

PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

Pipeline for annotating genomes using long read transcriptomics data with pinfish