502 Open source projects that are alternatives of or similar to pyrpipe

GREIN : GEO RNA-seq Experiments Interactive Navigator

Bystro genetic analysis (annotation, filtering, statistics)

Build and maintain multiple custom conda environments all in once place.

Ploidy agnostic phasing pipeline and algorithm

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

Predict plasmids from uncorrected long read data

Streamlining SLAM-seq analysis with ultra-high sensitivity

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

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

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

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

Feature extraction algorithm for genomic data

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

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

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

Real-time species-typing visualisation for nanopore data.

Assembling the cause of phenotypes and genotypes from NGS data

A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

Porting DESeq2 and DEXSeq into python via rpy2

The BridgeDb Library source code

SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data

Chanjo provides a better way to analyze coverage data in clinical sequencing.

Classify sequencing reads using MinHash.

GNparser normalises scientific names and extracts their semantic elements.

RNA-seq analysis pipeline for detection gene-fusions

A simple command-line tool to download data from Joint Genome Institute databases

Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).

pytoda - PaccMann PyTorch Dataset Classes. Read the docs: https://paccmann.github.io/paccmann_datasets/

conda recipes for freecad and dependencies of freecad

A permissively licensed library designed to replace Illumina's Experiment Manager

A modular annotation tool for genomic variants

Genomics using open source tools, running on GCP or AWS

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

Summer school course materials collection

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

Reference-based transcript discovery from long RNA read

A pipeline for the computational evaluation of RNA-Seq data

R mased batch sequence downloader, with primer development and in silico evaluation capabilities

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

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.

Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)

Improving genome bins through the combination of different binning programs

Single Cell Analysis Pipelines

Toolkit for preparing genomes for submission to NCBI

Rapid builds of small Conda-based containers using micromamba.

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

FEELnc : FlExible Extraction of LncRNA

Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

GRAph-based Finding of Individual Motif Occurrences

A workflow to build models of the European electricity system for Calliope.

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

🐍 Snakefiles for common RNA-seq data analysis workflows.

Computational Analysis of Novel Drug Opportunities

A handy variant calling pipeline generator for whole genome re-sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

An R package for reproducible and automated ADMIXTOOLS analyses