519 Open source projects that are alternatives of or similar to MetaOmGraph

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

Streamlining SLAM-seq analysis with ultra-high sensitivity

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

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

Reference-based transcript discovery from long RNA read

Pipeline for annotating genomes using long read transcriptomics data with pinfish

Single cell analysis in the browser

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

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

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

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

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

BACNET is a Java based platform to develop website for multi-omics analysis

Feature extraction algorithm for genomic data

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

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

GNparser normalises scientific names and extracts their semantic elements.

Genomics using open source tools, running on GCP or AWS

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

skimpy is a light weight tool that provides summary statistics about variables in data frames within the console.

Simple pure Python SAM parser and objects for working with SAM records

An R package for reproducible and automated ADMIXTOOLS analyses

FEELnc : FlExible Extraction of LncRNA

Computational Analysis of Novel Drug Opportunities

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

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

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

Command line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources

Golang for Bioinformatics

A faster lmm for GWAS. Supports GPU backend.

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

Improving genome bins through the combination of different binning programs

Toolkit for preparing genomes for submission to NCBI

Fast hash function for DNA sequences

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

📊 Codon usage tables in code-friendly format + Python bindings

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

A Kotlin DSL and library to create and plot RNA 2D structures

The Ensembl Compara Perl API and SQL schema

Digital Cell Sorter (DCS): single cell RNA-seq analysis toolkit. Documentation:

Read and write FASTQ and FASTA efficiently from Python

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

API for linked biological knowledge

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

Classify sequencing reads using MinHash.

Porting DESeq2 and DEXSeq into python via rpy2

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

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)

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

RNA-seq analysis pipeline for detection gene-fusions

Open source Java library for computational proteomics

Single Cell Analysis Pipelines

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

Insurance fraud claims analysis project

GRAph-based Finding of Individual Motif Occurrences

Summer school course materials collection

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.

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

ADENINE: A Data ExploratioN PipelINE