ARCHS4: All RNA and ChIP-Seq Sample and Signature Search

ARCHS4: All RNA and ChIP-Seq Sample and Signature Search

http://amp.pharm.mssm.edu/archs4/

pmr1 DR has exponential viability curve

Dr. Guo show that pmr1 DR has exponential survival curve, while YPD still have good Gompertz shape.

From H Guo:
"A quick test for pmr1-DR does show smaller AIC (3154.3) for the "exp" model than both "gompertz" (3155.0) and "weibull" (3155.9); meaning that the exponential model is more probable than Gompertz by 2 times, and than Weibull by 5 times."

single cell transcriptome analysis

single cell transcriptiome in aging mouse brain
https://www.nature.com/articles/s41593-019-0491-3?fbclid=IwAR1AZtVaFSyd_cNpzWpLoRjVUhYiu5WvTuYVR5Wz_DlUWRaePByTC5svsbA

single cell gene expression analysis
http://cole-trapnell-lab.github.io/monocle-release/docs/#installing-monocle

Student blackboard activity

Surprisingly, Sunday is one the best days that student complete online assignments.

EM example

https://youtu.be/XLKoTqGao7U

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

https://agingresearchbiobank.nia.nih.gov/studies/life/


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

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

UTC IT password management

https://www.utc.edu/information-technology/password.php

redirected to UTK password site.

goodness of fit test, gompertz model

http://www.tandfonline.com/doi/abs/10.1080/03610926.2014.892323

video education faculty network, youtube channel

http://tinyurl.com/video-eduction 

toread, big data

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

Free unix shell online

https://www.tutorialspoint.com/unix_terminal_online.php

deep convolutions learning

http://colah.github.io/posts/2014-07-Understanding-Convolutions/

Orange Pi

http://www.orangepi.org/orangepipc2/

NSF Bigdata

https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=504767