305 Open source projects that are alternatives of or similar to go_enrichment

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

Inference of switch-like differential expression along single-cell trajectories

use the noise

GA4GH Variation Representation Python Implementation

Explore gnomAD datasets on the web

A library for manipulating bioinformatics sequencing formats in Apache Spark

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Manhattan plot Generator

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

Finds SNP sites from a multi-FASTA alignment file

A Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.

Read HOMER motif analysis output in R.

Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

The GenePattern Server web application

Ultrafast sequence typing and gene detection from NGS raw reads

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

pathfindR: Enrichment Analysis Utilizing Active Subnetworks

CUT&RUN and CUT&Tag data processing and analysis

Forward-time simulation in Python using fwdpp

Collection of scripts for bacterial genomics

Introduction to the Command Line for Genomics

Performs memory-efficient reservoir sampling on very large input files delimited by newlines

Biopython Jupyter Notebook tutorial to characterize a small genome

A bioinformatics API and web-app to integrate multi-omics datasets & interface with public databases.

phenol: Phenotype ontology library

simple viewer for variant call format using htslib

Big Compute Learning Labs

A secure encryption tool for genomic data

Bead-based single-cell atac processing

Large genome reassembly based on Hi-C data, continuation of GRAAL

Bioconductor package for management of multi-assay data

Spatial alignment of single cell transcriptomic data.

A fast tool for hybrid genome assembly of long and short reads

DriverPower

Differential Gene Correlation Analysis

R package to access DoRothEA's regulons

Examples to get started with IBM Functional Genomics Platform

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data

Analysing Capture Seq Count Data

a pileup library that embraces the huge

Improve the quality of a denovo assembly by scaffolding and gap filling

Function prediction using a deep ontology-aware classifier

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

This repository contains the tensorflow implementation of "GNE: A deep learning framework for gene network inference by aggregating biological information"

Nextflow basic tutorial for newbie users

Genome Annotation Without Nightmares

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

Explore rearrangements and copy-number amplifications in a cancer genome

Phage-Host Interaction Search Tool

python library for working with ontologies and ontology associations

simuG: a general-purpose genome simulator

High-performance error correction for Illumina resequencing data

DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data

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

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.