Friday, September 22, 2017

custom distribution for flexsurvreg

##' ## Custom distribution
##' ## make "dEV" and "pEV" from eha package (if installed)
##' ##   available to the working environment
##' if (require("eha")) {
##' custom.ev <- list(name="EV",
##'                       pars=c("shape","scale"),
##'                       location="scale",
##'                       transforms=c(log, log),
##'                       inv.transforms=c(exp, exp),
##'                       inits=function(t){ c(1, median(t)) })
##' fitev <- flexsurvreg(formula = Surv(futime, fustat) ~ 1, data = ovarian,
##'                     dist=custom.ev)
##' fitev
##' lines(fitev, col="purple", col.ci="purple")
##' }


##'
##' ## Custom distribution: supply the hazard function only
##' hexp2 <- function(x, rate=1){ rate } # exponential distribution
##' hexp2 <- Vectorize(hexp2)
##' custom.exp2 <- list(name="exp2", pars=c("rate"), location="rate",
##'                     transforms=c(log), inv.transforms=c(exp),
##'                     inits=function(t)1/mean(t))
##' flexsurvreg(Surv(futime, fustat) ~ 1, data = ovarian, dist=custom.exp2)
##' flexsurvreg(Surv(futime, fustat) ~ 1, data = ovarian, dist="exp")
##' ## should give same answer

repositive.io genomics datasets


repositive.io

include 23&me, 1000 genomes, Allen institute, arrayexpress, corpasome

danish diabetes study, human DNA methylation

dbGap

EMI metagenomics

Encylopedia of DNA elements

Estonis biocentre
Europoean Aggregation consoritum

Expression atlas

Babriel

GEO
Genome Austria
Genome Asia 100K
Genome in a bottle
Genomes Unzipped
Giant consoritum
Horizon
Human genome diversity project
Human knockout project
insilicoDB
integrative japanese genome variant project

IHGC, international headache genetics consortium

DDBJ

Kadoorie biobank

Majic consoritum
Methylome DB

Mike's Genome Mike Lin

MTB, mouse tumor biology database

NGSmethDB
NIAGADS, NIA Alzheimer's Disease

Open Humans
Personal genome project
Repositive
SRA
Simons genome diversity project
Singapore Genome Variation project
Steven's Keating's genome
TACCF
Texax biobank
GONL
Biobank Finland
UCSC
Cancer Methylome system
Expressomics


Thursday, September 21, 2017

CALERIE

https://calerie.duke.edu/

Data only provided in SAS

student projects



=> yeast aging gene expression clustering -->  yeast network simulation. Yeast Histone methylation -> gene expression

Tuesday, September 5, 2017

toread, big data

http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=7406204