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Friends don't let friends make certain types of data visualization - What are they and why are they bad.

R 6,592 260 Updated Dec 10, 2024

Primer Pooler

C 12 1 Updated Feb 2, 2025

Please consider using/contributing to https://github.com/nf-core/scdownstream

Nextflow 24 11 Updated Jun 13, 2024

Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

Nextflow 251 181 Updated Feb 27, 2025

Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.

Nextflow 20 33 Updated Jan 27, 2025
JavaScript 8 1 Updated Nov 2, 2020

Composite LIkelihood eMpirical Bayes

R 8 2 Updated Oct 18, 2022

helper script to analyze nanopore run of umi data

Python 1 Updated Apr 23, 2022

Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers

Python 33 11 Updated Feb 27, 2024

Read overlap variant caller.

Python 7 1 Updated Apr 14, 2015

vSNP -- validate SNPs

Python 20 12 Updated Sep 19, 2024

Newest iteration of PurpleDrop. Reimplemented in kicad5

15 1 Updated Feb 15, 2022

TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain

C 27 4 Updated Jun 17, 2024

Reconstruction of transmission trees using genomic data

R 61 22 Updated Sep 27, 2023

Plotting tools for nanopore methylation data

Python 91 13 Updated May 24, 2024

SigMa is a probabilistic model for the sequential dependencies of mutation signatures

Python 17 7 Updated Jul 27, 2019
Python 9 1 Updated Nov 4, 2021

GAEseq: A Graph Auto-Encoder for Haplotype Assembly and Viral Quasispecies Reconstruction

C++ 7 Updated Jun 6, 2020

Visualise interstrain recombination from environmental samples.

Python 26 2 Updated Apr 18, 2019

diploid SNV caller for error-prone reads

Rust 197 26 Updated Apr 26, 2024

Segmented HAPlotype Estimation and Imputation Tool

C++ 91 18 Updated Aug 28, 2023

HapSeq2 release website

HTML 1 1 Updated Feb 9, 2017

phasing and Allele Specific Expression from RNA-seq

Python 111 35 Updated Jul 14, 2024

A python package storing different tools for different NGS operations

HTML 7 Updated Sep 13, 2021

QuantTB is a SNP based method to identify and quantify individual strains present in tuberculosis whole genome sequencing datasets.

Python 6 5 Updated Jul 6, 2023

List of software packages for multi-omics analysis

758 168 Updated Apr 23, 2024

vtreat is a data frame processor/conditioner that prepares real-world data for predictive modeling in a statistically sound manner. Distributed under choice of GPL-2 or GPL-3 license.

HTML 285 45 Updated Jan 9, 2025

Variant Ensemble Filter, an ensemble based filter for VCF files.

Python 6 Updated Nov 20, 2019
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