jbloom

I research the evolution of viruses and proteins.

Fred Hutchinson Cancer Research Center; Howard Hughes Medical InstituteSeattle, WA

Pinned Repositories

CoV_vs_flu_CFR
case fatality rates of COVI-19, 1918 influenza, seasonal influenza
Language:Jupyter Notebook4 2 12
epitopefinder
Python package for mapping epitopes to sequences
Language:Python6 4 05
Huanan_market_samples
Analysis of SARS-CoV-2 read counts versus metagenomic content for Huanan Seafood market sequencing data from Chinese CDC
Language:TeX5 2 02
SARS-CoV-2_PRJNA612766
Analysis of early Wuhan SARS-CoV-2 sequences from deleted SRA BioProject PRJNA612766
Language:HTML81 10 115
SARS2_28Dec2019_Genbank_submission
analysis of SARS-CoV-2 sequence submitted to Genbank on Dec-28-2019
Language:Jupyter Notebook12 1 10
dms_variants
Analyze deep mutational scanning of barcoded variants.
Language:Jupyter Notebook7 3 1210
neutcurve
Fit and plot neutralization curves
Language:Jupyter Notebook9 3 163
polyclonal
Model mutational escape from polyclonal antibodies.
Language:Jupyter Notebook3 7 600
SARS2-mut-fitness
Observed substitution counts of SARS-CoV-2 compared to those expected under the mutation rates
Language:Jupyter Notebook19 3 75
SARS2-RBD-escape-calc
SARS-CoV-2 RBD antibody escape calculator
Language:Jupyter Notebook11 1 12

jbloom's Repositories

jbloom/SARS-CoV-2_PRJNA612766
Analysis of early Wuhan SARS-CoV-2 sequences from deleted SRA BioProject PRJNA612766
Language:HTML81 10 115
jbloom/SARS2_28Dec2019_Genbank_submission
analysis of SARS-CoV-2 sequence submitted to Genbank on Dec-28-2019
Language:Jupyter Notebook12 1 10
jbloom/epitopefinder
Python package for mapping epitopes to sequences
Language:Python6 4 05
jbloom/Huanan_market_samples
Analysis of SARS-CoV-2 read counts versus metagenomic content for Huanan Seafood market sequencing data from Chinese CDC
Language:TeX5 2 02
jbloom/CoV_vs_flu_CFR
case fatality rates of COVI-19, 1918 influenza, seasonal influenza
Language:Jupyter Notebook4 2 12
jbloom/PRJNA692319_public
Analysis of Antarctica sequencing samples contaminated with SARS-CoV-2
Language:Python4 2 12
jbloom/SARS2-clade-spike-diffs
Plot spike differences among SARS-CoV-2 Pango clades
Language:Jupyter Notebook2 1 01
jbloom/eidith-1
⚠️ DEPRECATED ⚠️ Data is now at data.usaid.gov/Global-Health-Security-in-Development-GHSD-/PREDICT-Emerging-Pandemic-Threats-Project/tqea-hwmr
Language:R1 0 0
jbloom/Huanan_market_samples_addtl_analysis
additional analysis of metagenomic samples from the Huanan Seafood Market
Language:HTML1 1 10
jbloom/Omicron_clock
Molecular clock analysis on Omicron
Language:Jupyter Notebook1 1 0
jbloom/SARS-CoV-2_Shen_et_al
Language:Jupyter Notebook1 2 1
jbloom/SARS2-clock
Number of mutations relative to Wuhan-Hu-1 in SARS-CoV-2 clades
Language:Jupyter Notebook1 1 0
jbloom/alabaster
Lightweight, configurable Sphinx theme
Language:HTML0 0
jbloom/build_CritsChristoph_SARS2_seqs_tree
tree of sequences from Crits-Christoph et al (2024) paper
Language:Python1 0
jbloom/cluster_scripts
Scripts to investigate the SUKS cluster
Language:Python1 0
jbloom/COVID-19
Effect of genetic variants in COVID-19
Language:R1 0
jbloom/dms_tools
redirect to package hosted on jbloomlab
2 0
jbloom/DnaFeaturesViewer
:eye: Python library to plot DNA sequence features (e.g. from Genbank files)
Language:Python1 0
jbloom/epistasis
A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.
Language:Python2 0
jbloom/evofr
Tools for evolutionary forecasting
Language:Jupyter Notebook0 0
jbloom/GenomeSciences541
Lectures for Genome Sciences 541
Language:JavaScript2 04
jbloom/GS541-course-page
course webpage for Genome Sciences 541
Language:Python2 0
jbloom/GS541_epistasis_homework
demo and homework for Genome Sciences 541
Language:Jupyter Notebook1 0
jbloom/huanan-environmental
Language:Python1 0
jbloom/mapmuts
Map mutations and infer amino-acid preferences from overlapping paired-end amino acid reads
Language:Python5 02
jbloom/nextstrain.org
The Nextstrain website
Language:JavaScript1 0
jbloom/phyloExpCM
phylogenetic analyses with experimentally determined codon models
Language:Python3 03
jbloom/rebuild_Lv_SARS2_tree
Interactive phylogeny of early SARS-CoV-2 that attempts to reproduce Fig 3a of 2024 study by group of Yong-Zhen Zhang
Language:Jupyter Notebook1 0
jbloom/SC2_variant_rates
analyze substitution rate and mutation behavior within variants.
Language:TeX0 0
jbloom/snakemake
This is the development home of the workflow management system Snakemake. For general information, see
Language:Python1 0