Pinned Repositories
alignparse
Align sequences and then parse features.
CodonTilingPrimers
Create NNN primers tiling codons of a gene for codon mutagenesis
dms_tools2
software for the analysis and visualization of deep mutational scanning data
dmslogo
draw sequence logos tailored to deep mutational scanning (DMS) data
neutcurve
Fit and plot neutralization curves
phydms
phylogenetic analyses informed by deep mutational scanning data
SARS-CoV-2-RBD_DMS
Deep mutational scanning of the receptor-binding domain of SARS-CoV-2 Spike
SARS-CoV-2-RBD_DMS_variants
SARS2-mut-fitness
Observed substitution counts of SARS-CoV-2 compared to those expected under the mutation rates
SARS2_RBD_Ab_escape_maps
jbloomlab's Repositories
jbloomlab/SARS2-mut-fitness
Observed substitution counts of SARS-CoV-2 compared to those expected under the mutation rates
jbloomlab/alignparse
Align sequences and then parse features.
jbloomlab/phydms
phylogenetic analyses informed by deep mutational scanning data
jbloomlab/dmslogo
draw sequence logos tailored to deep mutational scanning (DMS) data
jbloomlab/SARS2-RBD-escape-calc
SARS-CoV-2 RBD antibody escape calculator
jbloomlab/neutcurve
Fit and plot neutralization curves
jbloomlab/dms_variants
Analyze deep mutational scanning of barcoded variants.
jbloomlab/reedmuenchcalculator
A python script for computing TCID50 using the Reed-Muench formula
jbloomlab/bench-to-byte
A biologist's guide to crafting quality code
jbloomlab/polyclonal
Model mutational escape from polyclonal antibodies.
jbloomlab/CoV_identities
Identities among SARS-CoV-2 variants and SARS-related coronaviruses
jbloomlab/Ab-CGGnaive_DMS
deep mutational scanning of the CGGnaive antibody
jbloomlab/Flu-HA-H5-2.3.4.4-DMS-informed-surveillance
Deep mutational scanning phenotypes of clade 2.3.4.4b influenza H5 HA
jbloomlab/MeV_SSPE_Dynamics
A spatial analysis of measles virus variant dynamics in the brain.
jbloomlab/SARS2-RBD-escape-mutants
designed escape mutants of the RBD of SARS-CoV-2 that contain potential future antigenic mutations
jbloomlab/ZIKV_DMS_NS3_EvansLab
Deep mutational scanning of Zika virus strain MR766 nonstructural protein 3 (NS3) with Matt Evans lab
jbloomlab/ZIKV_DMS_NS5_EvansLab
deep mutational scanning of ZIKV E protein +/- IFN with Matt Evans lab
jbloomlab/ZIKV_Y2H_198-209_combinatorial_library
jbloomlab/flu_seqneut_DRIVE_2021-22_repeat_vax
sequencing-based neutralization assays with H1N1 library against 2021-2022 DRIVE sera
jbloomlab/Herpesvirus-Glycoprotein-Analysis
Analysis of natural diversity in herpesvirus glycoproteins
jbloomlab/jbloomlab.github.io
A website for the Bloom lab
jbloomlab/seqneut-pipeline
Pipeline for analyzing sequencing-based neutralization assays
jbloomlab/binarymap
Binary representations of protein/nucleotide sequences.
jbloomlab/flu_seqneut_H3N2_2023-2024
sequencing-based neutralization assay on H3N2 HA variants from 2023-2024
jbloomlab/gga_codon_muts_oligo_design
Design oligos for Golden-Gate assembly mutagenesis
jbloomlab/SARS-CoV-2-RBD_MAP_Karolinska
jbloomlab/SARS-CoV-2-XBB.1.5_Spike_DMS_validations
jbloomlab/SARS-CoV-2_aerosol_bottleneck
Investigating how aerosol size impacts the SARS-CoV-2 transmission bottleneck.
jbloomlab/SARS2-cocktail-vax
Cocktail of SARS-CoV-2 spikes with predicted future mutation
jbloomlab/SARS2-spike-predictor-phenos
SARS-CoV-2 spike phenotypes (from DMS and other sources) potentially useful for predicting evolution