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38 search results found

Comp Genomics Class ⭐ 236

Code and examples for JHU Computational Genomics class

Serratus ⭐ 219

Ultra-deep search for novel viruses

pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)

Sequana ⭐ 136

Sequana: a set of Snakemake NGS pipelines

Code repository of the Earth Microbiome Project.

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

Sg Nex Data ⭐ 80

Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project

Sars Cov 2 Transcriptome ⭐ 76

Supplemental code for "the architecture of SARS-CoV-2 transcriptome" paper

Neoantigen Vaccine Pipeline ⭐ 72

Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines

xHLA: Fast and accurate HLA typing from short read sequence data

Pathogen Informatics Training ⭐ 38

Geofetch ⭐ 33

Builds a PEP from SRA or GEO accessions

Deeplexicon ⭐ 30

Signal based nanopore RNA demultiplexing with convolutional neural networks

High-throughput gene to knowledge mapping through massive integration of public sequencing data.

Framework for Metastatic And Clonal History INtegrative Analysis

Algorithms Dna Sequencing ⭐ 26

🧬 Algorithms for DNA Sequencing by Johns Hopkins University

Developments In Next Generation Sequencing ⭐ 25

Developments in next generation sequencing: instruments, read lengths, throughput. See

Isb_course_2022 ⭐ 22

Materials and presentation for the 2022 ISB Microbiome course.

Joint Trajectory Inference for Single-cell Genomics Using Deep Learning with a Mixture Prior

Desh Data ⭐ 22

Sequence lineage information extracted from RKI sequence data repo

Alignparse ⭐ 15

Align sequences and then parse features.

Sars Cov 2_sequencing ⭐ 13

SARS-CoV-2 Deep Sequencing

Micropheno ⭐ 11

MicroPheno Project

Singlecell_endodiff_paper ⭐ 11

Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

Amplimap ⭐ 11

amplicon/smMIP mapping and analysis pipeline

Python-based pipeline for analyzing Nanopore sequencing metabarcoding data

Exseqprocessing ⭐ 10

Isb_course_2023 ⭐ 10

Materials and presentation for the 2023 ISB Microbiome course.

Haplotype phaser for next-generation sequencing data

Factorizedembeddings ⭐ 7

Porekit Python ⭐ 7

A pythonic toolkit for working with Oxford Nanopore Data

2020_grant ⭐ 6

Code base for the Grant, Morales-Nebreda, and Markov et al., “Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia” Nature (2021) paper

Snplentiful ⭐ 6

SNP abundance correlates with network degree

Graph Iss ⭐ 5

Graph-based Decoding for In Situ Sequencing

Jupyter Notebooks to analyze T-cell Receptor Sequencing

Appliedgenomics2020 ⭐ 5

Description Materials for Spring 2020 Applied Genomics Course

Rrna_nanoshape ⭐ 5

Code accompanying "Direct detection of RNA modifications and structure using single molecule nanopore sequencing"

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