JacobKMcPherson
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Scientific programming
Accurate sample inference from amplicon data with single nucleotide resolution
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
R package for community ecologists: popular ordination methods, ecological null models & diversity analysis
phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. …
(No maintenance) Next Generation Sequencing Simulation with SNP, Variation and Sequencing Error Integrated
Processing and analysis of data coming from Illumina sequencing machines
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.
Cutadapt removes adapter sequences from sequencing reads
Tools (written in C using htslib) for manipulating next-generation sequencing data
Next generation sequencing reads de novo assembler.
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
A repository for setting up a RNAseq workflow
A PyTorch Basecaller for Oxford Nanopore Reads
Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network out…
Sequence correction provided by ONT Research
k-mer based Pipeline to identify the Serotype from Illumina NGS reads
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Open-source bioinformatics components for Dash
Collection of bioinformatics training materials
Windowed Adaptive Trimming for fastq files using quality
Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics
Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Immunology at The University of Michigan. This project seeks to…