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alicecsq

alicecsq

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snippy

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cutrun_nf

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Pasteur-canteen-desserts

A Survey of Canteen Desserts at Institut Pasteur

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quantify-snrna

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slack

Bring your code to the conversations you care about with the GitHub and Slack integration

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book

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genbioconductor

Materials for Genomics Data Science: Introduction to Bioconductor

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Whole_Transcriptome_Paper

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sc-da-parkinsons

Data and code for "Single-Cell RNA-Seq of Mouse Dopaminergic Neurons Informs Candidate Gene Selection for Sporadic Parkinson Disease" (Hook, 2018)

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sn-code

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genomic-data-visualization-2022

Course website for Genomic Data Visualization 2022

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fasteR

Fast Lane to Learning R!

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spatialLIBD

Code for the spatialLIBD R/Bioconductor package and shiny app

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TAQLoRe

TAQLoRe - Transcript Annotation and Quantification using Long Reads

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awesome-nanopore

A curated list of awesome nanopore analysis tools.

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LongRead_tutorials

Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data

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UpSetR

An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..

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C1-CAGE-preview

Technology preview of the C1 CAGE protocol: processing and quality control.

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R_nanopore

R package for analysing nanopore data

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LIQA

Long-read Isoform Quantification and Analysis

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bambu

Reference-guided transcript discovery and quantification for long read RNA-Seq data

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stringtie2

Transcript assembly and quantification for RNA-Seq

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nanoseq

Nanopore demultiplexing, QC and alignment pipeline

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appliedgenomics2018

Materials for Spring 2018 Applied Genomics Course

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applied-computational-genomics

Applied Computational Genomics Course at UU: Spring 2020

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SpatialExperiment_Bioc2021

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PCAworkshop

An introduction to matrix factorization and PCA and SVD.

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rapids-single-cell-examples

Examples of single-cell genomic analysis accelerated with RAPIDS

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megalodon

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 output to a reference genome/transriptome.

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bonito

A PyTorch Basecaller for Oxford Nanopore Reads

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