172 Open source projects that are alternatives of or similar to snakefiles

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

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

Fast and accurate gene fusion detection from RNA-Seq data

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Deep Learning based cell composition analysis with Scaden.

Code and more for the QUB Development Weeks event 'High Performance Python'

A system for development of high-performance, data-intensive, distributed computing, applications, tools, and libraries.

Single cell analysis in the browser

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

A versatile sequenced read processor for nanopore direct RNA sequencing

Fast and easy parallel mapreduce on HPC clusters

A code for fast, massively-parallel direct numerical simulations (DNS) of canonical flows

Everything about low latency system.

Lightweight and Fast; RNA-seq quantification at the event-level

Performant time measuring in Rust

[MIRROR] Emacs support for Snakemake

Scripts to import your FeatureCounts output into DEXSeq

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

📊 Graphical User Interface for TCC package

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

Linnea is an experimental tool for the automatic generation of optimized code for linear algebra problems.

Sympiler is a Code Generator for Transforming Sparse Matrix Codes

Parallel algorithms and data structures for tree-based AMR with arbitrary element shapes.

A robust, extensible metagenomics pipeline

Next-Gen Sequencing tools from the Horvath Lab

A proof of concept RNA-Seq pipeline with Nextflow

Library for steering campaigns of simulations on supercomputers

Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.

Quickly generate, start and analyze benchmarks for molecular dynamics simulations.

A Flexible Storage Framework for HPC

CWL tools and workflows for GGR

A graphical user interface for distributed data processing of high throughput genomics

GREIN : GEO RNA-seq Experiments Interactive Navigator

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

Domain-specific compiler for Finite Difference/Volume/Element Earth-system models in Fortran

Pseudofermion functional renormalization group solver for (frustrated) quantum magnets in two and three spatial dimensions.

Automatic optimization and parallelization for Scientific Machine Learning (SciML)

A minimal example data analysis project with the targets R package

An automated RNA-seq pipeline using Nextflow

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

Multi-omics analysis protocols by Lyu.

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

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

Pipeline for annotating genomes using long read transcriptomics data with pinfish

Snakemake based pipeline for RNA-Seq analysis

HiCMA: Hierarchical Computations on Manycore Architectures

Monitor computational workflows in real time

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

Fast in-silico normalization algorithm for NGS data

Amplicon sequence processing workflow using QIIME 2 and Snakemake

This is the second part of the Deep Learning Course for the Master in High-Performance Computing (SISSA/ICTP).)

Differential Gene Correlation Analysis

A workflow for creating small NGS test data sets, useful for continuous integration.

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

CRAN Task View: Model Deployment with R

development repository for the open earth compiler

Reproducible Bayesian data analysis pipelines with targets and cmdstanr

Desktop/Android Python game development framework on top of Vulkan API

Massive-Parallel Trajectory Calculations (MPTRAC) is a Lagrangian particle dispersion model for the analysis of atmospheric transport processes in the troposphere and stratosphere.

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders