569 Open source projects that are alternatives of or similar to Smudgeplot

Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests

A full spaCy pipeline and models for scientific/biomedical documents.

Compressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGen…

Introduction to the Unix Shell for biologists

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

A standard implementation conforming to the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification and a web application for managing and executing those WES services.

Multilocus sequence typing by blast using the schemes from PubMLST

A collaboratively written review paper on deep learning, genomics, and precision medicine

🐳 Bio-dockers: dockerized bioinformatic tools

Sample search by metadata and features

Numerical Encoding for Human Genetic Variants

🐣 locally query the ncbi taxonomy

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

WebLogo 3: Sequence Logos redrawn

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

For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml

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

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

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

The Microbiome Interpretable Temporal Rule Engine

Python-based UCSC genome browser snapshot-taker and gallery-maker

Parser and database to index the terpene profile of different strains of Cannabis from online databases

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.

A simplified pipeline for ctDNA sequencing data analysis

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

CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies

Explore rearrangements and copy-number amplifications in a cancer genome

De novo genome assembly and multisample variant calling

Bead-based single-cell atac processing

Pan-genome wide association studies

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

The Ontology for Biomedical Investigations

Fast & accurate alignment of barcoded short-reads

Toolkit for processing sequences in FASTA/Q formats

Introduction to Applied Mathematics and Informatics in Drug Discovery (AMIDD)

Analysing Capture Seq Count Data

micca - MICrobial Community Analysis

Mapping-Assisted Targeted-Assembly for Metagenomics

Support Vector Structural Variation Genotyper

tools for working with genome variation graphs

Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝

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

ntHash implementation in Rust

(No maintenance) Detect gene fusion directly from raw fastq files

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

No description or website provided.

MOLGENIS - for scientific data: management, exploration, integration and analysis.

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

Curated list of bioinformatics formats and publications

use the noise

A Suite of Packages for Analysis of Big Genomic Data

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

Aggregate results from bioinformatics analyses across many samples into a single report.

Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format

Emperor a tool for the analysis and visualization of large microbial ecology datasets

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

A library to build and execute typed scientific workflows

exploratory and interactive microbiome analyses based on heatmaps

A plotly.js React component from Plotly 📈