vjcitn

FROM ubuntu:jammy

LABEL org.label-schema.license="GPL-2.0" \
      org.label-schema.vcs-url="https://github.com/rocker-org/" \
      org.label-schema.vendor="Rocker Project" \
      maintainer="Dirk Eddelbuettel <[email protected]>"

## Set a default user. Available via runtime flag `--user docker`
## Add user to 'staff' group, granting them write privileges to /usr/local/lib/R/site.library
## User should also have & own a home directory (for rstudio or linked volumes to work properly).

vjcitn

library(shiny)
colorapp2 = function () 
{
    colordot = function (r, g, b) {
        plot(0, 0, col = grDevices::rgb(r, g, b), pch = 19, cex = 15)
    }

    ui = fluidPage(
          sidebarLayout(
           sidebarPanel(

vjcitn

library(shiny)
library(imager)
mpath = "https://mghp.osn.xsede.org/bir190004-bucket01/BiocGeneralData/mast.jpg"
happ = function () {
  ui = fluidPage(
   sidebarLayout(
   sidebarPanel(
    helpText("slider for cannyEdges alpha"), 
    sliderInput("alpha", "alpha", min = 0, max = 1, step = 0.05, 

vjcitn

#' produce an ontology_index instance from semantic sql sqlite connection
#' @param con DBI::dbConnect value for sqlite table
#' @return result of ontologyIndex::ontology_index evaluated for the labels and 
#' parent-child relations in tables statements and edge of the semantic sql resource
#' @export
semsql_to_oi = function(con) {
# sqlite> select * from statements where predicate = 'rdfs:label' limit 40;
 alltabs = DBI::dbListTables(con)
 stopifnot(all(c("edge", "statements") %in% alltabs))
 labdf = dplyr::tbl(con, "statements") |> dplyr::filter(predicate == "rdfs:label") |>

vjcitn

stopifnot(Sys.getenv("_R_CHECK_SUGGESTS_ONLY_") == "true")
# these error in check on nebbiolo2 but not lconway

suggposs = c("AffyRNADegradation", "alabaster.spatial", "ANF", "animalcules", 
"BDMMAcorrect", "bnbc", "CancerSubtypes", "ccrepe", "CDI", "cellscape", 
"ClassifyR", "CNVgears", "CoGAPS", "compartmap", "CoRegNet", 
"crisprseekplus", "DEWSeq", "DEXSeq", "DMCFB", "dpeak", "DSS", 
"EasyCellType", "eegc", "EGSEA", "EpiCompare", "exomePeak2", 
"farms", "FCBF", "flowMap", "FoldGO", "FScanR", "GCSscore", "GenomicFeatures", 
"GEOmetadb", "GEOquery", "gscreend", "HelloRanges", "ILoReg", 

vjcitn

# assumes https://github.com/biocypher/igan.git README instructions
# followed, docker compose up -d succeeded and localhost:7474 gives
# a neo4j browser interface (at localhost:7687/browser on my machine)
#
# BiocManager::install("neo4j-rstats/neo4r")
# want 0.1.3
library(neo4r)
library(magrittr)
con <- neo4j_api$new(
  url = "http://localhost:7474", user="", password="")

vjcitn

# a replacement for library() that does not print tons of messages
# as each package is loaded.  place in .Rprofile

libstats = function(inisess, newsess) {
 inibase = inisess$basePkgs  # unchanging?
 inioth = names(inisess$otherPkgs)
 newbase = newsess$basePkgs
 newoth = names(newsess$otherPkgs)
 iniatt = length(unique(c(inibase,inioth)))
 newatt = length(unique(c(newbase,newoth)))

vjcitn

library(shiny) # works with the chr22.vcf.gz in the VariantAnnotation extdata
library(dplyr)
library(DT)
library(VariantAnnotation)
library(BSgenome.Hsapiens.UCSC.hg19)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

ui <- fluidPage(
  titlePanel("VCF XPLORR"),
  numericInput("numvar", "num2chk", value = 50, min = 50, max = 500, step = 10),

vjcitn

#
# https://priyanshwarke2015-ndcs.medium.com/image-classification-with-cnn-model-in-cifar100-dataset-8d4122b75bad
# with user-level miniconda3 installed, use
# miniconda3/bin/pip install matplotlib
# miniconda3/bin/pip install torchvision


import os
import torch
import torchvision