346 Open source projects that are alternatives of or similar to GCModeller

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

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

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netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

Earl Grey: A fully automated TE curation and annotation pipeline

Example client programs for Saphetor's VarSome annotation API

mgatk: mitochondrial genome analysis toolkit

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PETAL (ParallEl paThways AnaLyzer): a Python tool for deep biological pathway analysis

Análisis de texto y visualización de datos con R, de conversaciones de WhatsApp, primer parte. Uso de librería rwhatsapp.

Ultrafast sequence typing and gene detection from NGS raw reads

Manhattan plot Generator

Transcripts annotation and GO enrichment Fisher tests

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Tools for single-cell data processing

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

The EXASOL package for R provides an interface to the EXASOL database.

VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps

ntHash implementation in Rust

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Nextflow basic tutorial for newbie users

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

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Examples to get started with IBM Functional Genomics Platform

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Spark VCF data source implementation for Dataframes

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

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

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.

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

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

Efficient genotyping bi-allelic SNPs on single cells

A library for manipulating bioinformatics sequencing formats in Apache Spark

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

Identify phage regions in bacterial genomes for masking purposes

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

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

Pipeline for annotating genomes using long read transcriptomics data with pinfish

simple viewer for variant call format using htslib

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

GA4GH Variation Representation Python Implementation

A secure encryption tool for genomic data

Kaggle Kernels (Python, R, Jupyter Notebooks)

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

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

WebAssembly modules for genomics

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

Forward-time simulation in Python using fwdpp

use the noise

The GenePattern Server web application

Explore rearrangements and copy-number amplifications in a cancer genome

DriverPower

Convert between AnnData and SingleCellExperiment