2019-09-10 fad2d50d4084cd610692123903bbe72cb6abc2fc
2019-08-13 welch16
updating codes and stuff
tree@ a9d42c commitdiff
2019-07-11 welch16
finished an preliminary run of the breast cancer analysis
tree@ 3e9624 commitdiff
2019-06-28 welch16
wrote scripts to add many group lasso like models
tree@ 8a169c commitdiff
2019-06-19 welch16
re-processed models to center and scale before, and added an exploration of...
tree@ c55d99 commitdiff
2019-06-03 welch16
wrote script to fit predictive models / with the baseline penalty or adapti...
tree@ a5f311 commitdiff
2019-02-20 welch16
added venn diagrams to the document, showing that there is an error in the ...
tree@ 21a48d commitdiff
2019-02-20 welch16
added search for snp positions from rs ids
tree@ 620714 commitdiff
2019-02-19 welch16
started notebook comparing snp sets
tree@ c07f49 commitdiff
2019-02-14 welch16
added note on the new distribution of survey variables
tree@ f0e25d commitdiff
2019-02-04 welch16
fixed irene's corrections and added a few more plots
tree@ 19565b commitdiff
2019-02-01 welch16
finished analysis of genotype for the email
tree@ f52f40 commitdiff
2019-01-29 welch16
found issue with some mayo snps
tree@ e9f63c commitdiff
2019-01-28 welch16
updated the code to check genotype quality scores too
tree@ d36104 commitdiff
2019-01-16 welch16
added comentary
tree@ 645223 commitdiff
2019-01-15 welch16
wrote code to calculate the GQ of vcf file based on the plexseq aligned data
tree@ ee5cda commitdiff
2019-01-14 welch16
wrote a description of how to calculate the GQ field out of aligned reads
tree@ a66b2f commitdiff
2019-01-14 welch16
added another method to the note GFLasso
tree@ 68b916 commitdiff
2019-01-14 welch16
adding note on the tree-lasso method
tree@ 6c8c64 commitdiff
2019-01-11 welch16
added comparison on # aligned distributions for each snp
tree@ af3b9e commitdiff
2019-01-10 welch16
adding empty ref file
tree@ 33c797 commitdiff
2019-01-09 welch16
re-wrote the document
tree@ 3371fc commitdiff
2019-01-09 welch16
started QC document
tree@ 4cca0b commitdiff
2019-01-09 welch16
draw diagram to explain possible bottlenecks in the data generation procedure
tree@ de1a44 commitdiff
2019-01-08 welch16
wrote paragraph on the assumptions that we may need in the idea
tree@ 0ea62e commitdiff
2019-01-08 welch16
changed missing % barplot from notebook, to keep all missing data analysis ...
tree@ 83ea0a commitdiff
2019-01-07 welch16
tree@ 44df90 commitdiff
2019-01-07 welch16
wrote a generalization idea of the structure lasso
tree@ 25fd9d commitdiff
2019-01-04 welch16
minor fix
tree@ 7f2049 commitdiff
2018-12-21 welch16
init commit converting plexseq to vcf
tree@ c83eb3 commitdiff
2018-12-19 welch16
updated results to include also large k runs for knn-impute
tree@ 4c97fa commitdiff
2018-12-18 welch16
wrote code to evaluate different imputation methods
tree@ 1e3403 commitdiff
2018-12-14 welch16
added code to perform knn-mice impute and run multiple versions in condor
tree@ ca2dd7 commitdiff
2018-12-12 welch16
added description to the experiment
tree@ fde4f1 commitdiff
2018-12-07 welch16
reviewed breast density data, and included 2 alternatives for the breast de...
tree@ f652cc commitdiff
2018-12-06 welch16
explored the paired variables amy mentioned, checked the breast density stu...
tree@ 1754f7 commitdiff
2018-12-05 welch16
added two more sections for future work
tree@ eec03d commitdiff
2018-12-05 welch16
added document reviewing the data cleaning issues discussed in the last mee...
tree@ 022057 commitdiff
2018-11-30 welch16
wrote a report trying the re-engineer the algorithms used to call genotypes...
tree@ 2da5b3 commitdiff
2018-11-29 welch16
added functions to convert from plexseq format to vcf
tree@ f7a28c commitdiff
2018-11-28 welch16
added analysis exploring the number of reads necessary to call snps
tree@ aacf5c commitdiff
2018-11-28 welch16
finished the analysis of the mayo snps with more than 1 alternative alleles
tree@ 41c711 commitdiff
2018-11-28 welch16
changed name of file
tree@ 64d329 commitdiff
2018-11-27 welch16
pre-commit mayo counts
tree@ d01962 commitdiff
2018-11-16 welch16
tried to create artificial pROC objects to calculate tests but failed
tree@ 850783 commitdiff
2018-11-16 welch16
added other svm method comparison
tree@ ae452d commitdiff
2018-11-15 welch16
finish slides
tree@ 6967cc commitdiff
2018-11-14 welch16
updated some plots in the markdown file
tree@ 906ea8 commitdiff
2018-11-14 welch16
removed person_id from feature files
tree@ f7f3c1 commitdiff
2018-11-13 welch16
added shuffle options to python codes to fix the low accuracy issue
tree@ ad9690 commitdiff
2018-11-13 welch16
adding more slides and changed priority to have mayo snps first
tree@ 615664 commitdiff
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