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/phydms
phylogenetic analyses informed by deep mutational scanning data
jbloomlab/CodonTilingPrimers
Create NNN primers tiling codons of a gene for codon mutagenesis
jbloomlab/SARS-CoV-2-RBD_MAP_HAARVI_sera
Mutational antigenic profiling of SARS-CoV-2 RBD against human convalescent sera from the HAARVI cohort
jbloomlab/SARS-CoV-2-RBD_MAP_Crowe_antibodies
Mutational antigenic profiling of Crowe-lab antibodies to SARS-CoV-2 RBD
jbloomlab/pdb_prot_align
Align proteins to chains in PDB structures
jbloomlab/CoV_229E_antigenic_drift
jbloomlab/SARS-CoV-2-RBD_MAP_Rockefeller
Analysis of mutational antigenic profiling of SARS-CoV-2 RBD against monoclonal antibodies and convalescent patient sera from a NYC cohort.
jbloomlab/SARS-CoV-2_lentiviral_pseudotype
pseudotyping lentiviral virions with SARS-CoV-2 Spike
jbloomlab/EnvMutationalShiftsPaper
Hugh's paper on shifting mutational effects in HIV Env
jbloomlab/HA_antibody_ease_of_escape
comparison of ease of escape of WSN influenza from various narrow and broad anti-HA antibodies
jbloomlab/SARS-CoV-2-RBD_MAP_clinical_Abs
Mutational antigenic profiling of SARS-CoV-2 RBD against REGN-COV2 and LY-CoV016
jbloomlab/human-CoV-antigenic-drift-references
papers / background on human seasonal CoV antigenic drift
jbloomlab/SARS-CoV-2-RBD_MAP_Moderna
jbloomlab/SARS-CoV-2_chronic-infection-seq
Analysis of SARS-CoV-2 deep-sequencing runs from an immunocompromised patient.
jbloomlab/cookiecutter-pypackage
Cookiecutter template for a Python package.
jbloomlab/COVID-19
Effect of genetic variants in COVID-19
jbloomlab/dms-view-ms
Manuscript describing the `dms-view` visualization tool
jbloomlab/dms_db
jbloomlab/egg_adaptation_Perth2009_HA
Trying to identify egg adaptation mutations in H3 HA by deep mutational scanning
jbloomlab/jbloomlab.github.io
A website for the Bloom lab
jbloomlab/map_flu_serum_Vietnam_H3_Perth2009
mutational antigenic profiling of 2010-2011 Vietnam serum samples against Perth/2009 (H3N2)
jbloomlab/PB2_Pimodivir_Resistance
jbloomlab/pilot_experiment
jbloomlab/RBD_nanoparticle_vaccine
jbloomlab/SARS-CoV-2-RBD_MAP_AZ_Abs
Mutational antigenic profiling of AZD8895 and AZD1061
jbloomlab/SARS-CoV-2-RBD_MAP_Ellebedy_Abs
Mutational antigenic profiling of RBD escape mutations from Ali Ellebedy antibodies tested in vivo
jbloomlab/SARS-CoV-2-RBD_MAP_RBD-nano-vax-NHP1
jbloomlab/SARS-CoV-phydms
phylogenetic analysis of SARS-CoV sequences using deep mutational scanning data
jbloomlab/TargetedTilingPrimers
Create mutation targeting primers tiling codons of a gene for codon mutagenesis
jbloomlab/Vacc_Rabbit_Sera_MAP