Pinned Repositories
cancereffectsizeR
cancereffectsizeR: Estimate somatic mutation rates and quantify selection in cancer
CSIMAC-1
glioma_CES
HNSCC_APOBEC
Analyses for our Oncogene manuscript here: https://www.nature.com/articles/s41388-018-0657-6. Analyses accessed in the markdown file here: https://github.com/Townsend-Lab-Yale/HNSCC_APOBEC/blob/master/APOBEC_HNSCC_manuscript_analysis.md
KRAS_G12C_analysis
Analysis within The likelihood of heterogeneity or additional mutation in KRAS or associated oncogenes to compromise targeting of oncogenic KRAS G12C
LUAD-PhyLCT
Code and data for local consolidative treatement with Mahal and Yu.
MASSPRF
neutral_theory_somatic_evo
pALL-mutation-effects
Analysis of cancer effect in pediatric B-ALL and T-ALL, based on data from Brady 2022 (Nature Genetics)
SNV_selection_intensity
Analyses associated with manuscript https://www.biorxiv.org/content/early/2018/02/27/229724 ... updated pipeline with R package here: https://github.com/Townsend-Lab-Yale/cancereffectsizeR
Townsend Lab, Yale School of Public Health's Repositories
Townsend-Lab-Yale/cancereffectsizeR
cancereffectsizeR: Estimate somatic mutation rates and quantify selection in cancer
Townsend-Lab-Yale/KRAS_G12C_analysis
Analysis within The likelihood of heterogeneity or additional mutation in KRAS or associated oncogenes to compromise targeting of oncogenic KRAS G12C
Townsend-Lab-Yale/LUAD-PhyLCT
Code and data for local consolidative treatement with Mahal and Yu.
Townsend-Lab-Yale/pALL-mutation-effects
Analysis of cancer effect in pediatric B-ALL and T-ALL, based on data from Brady 2022 (Nature Genetics)
Townsend-Lab-Yale/SNV_selection_intensity
Analyses associated with manuscript https://www.biorxiv.org/content/early/2018/02/27/229724 ... updated pipeline with R package here: https://github.com/Townsend-Lab-Yale/cancereffectsizeR
Townsend-Lab-Yale/cancer-epistasis
Mathematical model to estimate mutation origination and fixation dependent on somatic cancer genotypes
Townsend-Lab-Yale/glioma_CES
Townsend-Lab-Yale/HNSCC_APOBEC
Analyses for our Oncogene manuscript here: https://www.nature.com/articles/s41388-018-0657-6. Analyses accessed in the markdown file here: https://github.com/Townsend-Lab-Yale/HNSCC_APOBEC/blob/master/APOBEC_HNSCC_manuscript_analysis.md
Townsend-Lab-Yale/journal_targeter
Web app for journal suitability metrics, based on manuscript title, abstract and references.
Townsend-Lab-Yale/MASSPRF
Townsend-Lab-Yale/neutral_theory_somatic_evo
Townsend-Lab-Yale/ADTEx
ADTEx fork, for use with cnv_pipeline
Townsend-Lab-Yale/cancer_causes_and_effects
Townsend-Lab-Yale/ces.refset.hg19
Data package for use with cancereffectsizeR
Townsend-Lab-Yale/ces.refset.hg38
Data package for use with cancereffectsizeR
Townsend-Lab-Yale/Integrated_LUAD_Data_and_Code
A comprehensive LUAD dataset of 9424 samples with whole-genome sequence data (WGS), whole-exome sequence data (WES), and targeted sequence data (TGS), including 1082 smokers and 642 never-smokers.
Townsend-Lab-Yale/lung-smoking
To study the mutational and adaptive landscape of LUAD and how it is altered by tobacco smoke using an aggregated LUAD dataset
Townsend-Lab-Yale/MathematicaCodesForTemporalInference
Townsend-Lab-Yale/QTL-MA-test-for-selection
Townsend-Lab-Yale/sbs18_aml
Analysis of contribution of SBS18 to acute myeloid leukemia
Townsend-Lab-Yale/cnv_pipeline
Automated copy number analysis using ADTEx and saasCNV
Townsend-Lab-Yale/lift_coords
Basic Python wrapper for LiftOver
Townsend-Lab-Yale/LUSC_APOBEC_NFE2L2_ms
Townsend-Lab-Yale/massprf-pipeline
pipeline for genome wide MASSPRF analysis
Townsend-Lab-Yale/massprf-protein-coloring
maps the output of massprf into a file that can be used in Chimera to color proteins
Townsend-Lab-Yale/MASSPRF_demo_simulations
Townsend-Lab-Yale/P0PCorNS
P0PCorNS: Perturbation to 0 to Predict Correlated Network Stability
Townsend-Lab-Yale/paad-mapk-drivers
Townsend-Lab-Yale/Ultimate_Signal_Noise
Townsend-Lab-Yale/VirusScan
VirusScan Pipeline