2019-09-10 fad2d50d4084cd610692123903bbe72cb6abc2fc
2019-09-10 welch16
adding emca4 interaction analysis to see if it improves prediction performa...
tree@ fad2d5 commitdiff
2019-08-14 welch16
amia paper submit
tree@ 4d5e88 commitdiff
2019-08-13 welch16
results file, with comparisons of cases and controls
tree@ 0ed469 commitdiff
2019-08-13 welch16
updating codes and stuff
tree@ a9d42c commitdiff
2019-07-23 welch16
finished imputation of missing values
tree@ b4a8d7 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
2019-05-28 welch16
wrote script to parse and impute the data into matrices
tree@ 8495c9 commitdiff
2019-05-07 welch16
wrote code to impute survey missing at random values
tree@ b71ded commitdiff
2019-05-06 welch16
wrote code to clean survey data
tree@ 83f690 commitdiff
2019-04-18 welch16
added script to clean all at the snp levels
tree@ 5b5f2b commitdiff
2019-04-05 welch16
wrote script to change the new mayo data from vcf to Rdata, and then query ...
tree@ d3c6e8 commitdiff
2019-03-20 welch16
Added line to impute with condor
tree@ c14bde commitdiff
2019-03-20 welch16
script to convert / process / prepare vcf files for imputation
tree@ bc533f commitdiff
2019-03-20 welch16
removed indels because they are not in the BC77 set
tree@ ec2122 commitdiff
2019-03-20 welch16
changed name
tree@ 71ec13 commitdiff
2019-03-20 welch16
added failed pipeline to impute with impute2
tree@ d8112f commitdiff
2019-03-15 welch16
adding script to convert to oxford format for imputation
tree@ 0334ec commitdiff
2019-03-15 welch16
finished formats
tree@ 97e26b commitdiff
2019-03-13 welch16
renamed files and directories to make it more consistent
tree@ c30c20 commitdiff
2019-03-13 welch16
added code to change the format of the snp data
tree@ 703b9e commitdiff
2019-02-22 welch16
updated the rievew with one more current paper, and added a quick analysis ...
tree@ afabe4 commitdiff
2019-02-21 welch16
added lines to liftover the 313 snps
tree@ 099f43 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
2019-02-19 welch16
added tibble of the 313 brest cancer snps of Mavaddat et al
tree@ 9338ff commitdiff
2019-02-19 welch16
added a common set test on the method
tree@ 864183 commitdiff
2019-02-01 welch16
finished analysis of genotype for the email
tree@ f52f40 commitdiff
2019-01-28 welch16
updated the code to check genotype quality scores too
tree@ d36104 commitdiff
2019-01-24 welch16
added script that gets the snp - sample combination with failed genotype an...
tree@ e32744 commitdiff
2019-01-15 welch16
wrote code to calculate the GQ of vcf file based on the plexseq aligned data
tree@ ee5cda commitdiff
2019-01-11 welch16
wrote script to calculate the frequency occurrences of all bases in a set o...
tree@ 9aea19 commitdiff
2019-01-10 welch16
fixed code to align with bowtie2 and then convert and sort with samtools in...
tree@ b901cc commitdiff
2019-01-09 welch16
wrote script to align samples with bowtie2 in condor
tree@ 694644 commitdiff
2019-01-09 welch16
wrote script to generate samples to use for the QC test
tree@ f6107e commitdiff
2019-01-04 welch16
finished the script to convert from plexseq format into vcf files
tree@ 91e948 commitdiff
2019-01-04 welch16
added a pair of snps that had to be manually curated, because they weren't ...
tree@ 38dd5a commitdiff
2019-01-03 welch16
fixed error, where genotypes without values or fail weren't being parsed to...
tree@ 219a45 commitdiff
2019-01-03 welch16
a lot of plexseq snps were being removed, so changed the script to only fil...
tree@ cf22d1 commitdiff
2019-01-03 welch16
included the reference and alternative counts to the data set
tree@ 834ec4 commitdiff
2019-01-03 welch16
updated slides by including the knn imputation results
tree@ 261b08 commitdiff
2019-01-03 welch16
aux commit to change name
tree@ e37741 commitdiff
2019-01-03 welch16
added script to process repeated samples due to the change in the mayo file...
tree@ 58b508 commitdiff
2018-12-28 welch16
added more reviews
tree@ 9aae5c 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
2018-12-19 welch16
added script to perform large k nearest neighbor imputation
tree@ d045ca commitdiff
2018-12-18 welch16
wrote code to evaluate different imputation methods
tree@ 1e3403 commitdiff
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