Vince Carey vjcitn
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| do_SingleRi = function(sce=NULL, path="/home/vincent/tenx3k.h5ad", | |
| ref=celldex::HumanPrimaryCellAtlasData(), | |
| ref.type = "label.main", | |
| min.common = 1000, assay.type.test=1L, instrument=TRUE, | |
| clprocid=NULL, ...) { | |
| if (instrument == TRUE && is.null(clprocid)) stop("clprocid not set") | |
| cl_timestamp(clprocid, "init") | |
| stopifnot(ref.type %in% c("label.main", "label.fine")) | |
| if (is.null(sce)) { | |
| is_h5ad = length(grep("h5ad$", path)==1) |
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| source("inst.R", echo=TRUE) | |
| library(Rcollectl) | |
| library(AnVILBestPractices) | |
| library(SingleR) | |
| library(BiocParallel) | |
| clid = cl_start() | |
| Rcollectl::cl_timestamp(clid, "pre-data") | |
| p3k = TENxPBMCData::TENxPBMCData("pbmc3k") | |
| Rcollectl::cl_timestamp(clid, "3k loaded") | |
| rownames(p3k) = make.names(rowData(p3k)$Symbol, unique=TRUE) |
vjcitn
/ probe_lake.R
Created
March 15, 2024 13:26
defines a function probe_lake() to produce shiny app to explore BiocBuildDB data lake
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| # setup | |
| library(aws.s3) | |
| library(DBI) | |
| library(dplyr) | |
| library(duckdb) | |
| library(shiny) | |
| # get bucket content metadata into a data.frame "bb" |
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| con <- dbConnect(duckdb::duckdb(), read_only=TRUE) | |
| dbExecute(con, "install 'httpfs'") | |
| dbExecute(con, "load 'httpfs'") | |
| library(ggplot2) | |
| devinf = "buildResults/f9785dba87426695825cc6524dcb82c6-info.csv.gz" | |
| pa = sprintf('s3://bioc-builddb-mirror/%s', devinf) | |
| sqlstring = sprintf("FROM read_csv('%s')", pa) |
vjcitn
/ pull_info.R
Created
March 11, 2024 11:08
code to explore info.csv collected by BiocBuildDB process
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| allinf = c( | |
| "buildResults/08150976a8cce9f7bf2d08a6ff86160c-info.csv.gz", | |
| "buildResults/19dfe90f431098a035502d632404e0f2-info.csv.gz", | |
| "buildResults/27dc71f7942ea33a660ca2495d2701d0-info.csv.gz", | |
| "buildResults/2a0158be35acdff034889a8b072b823d-info.csv.gz", | |
| "buildResults/2cc2a659a35d607f71655f3c9c9e4283-info.csv.gz", | |
| "buildResults/3ebd0a185863d3d036726be357bedc60-info.csv.gz", | |
| "buildResults/4104e02fcdf0685bf51735c7abb2c06e-info.csv.gz", | |
| "buildResults/519f35883478df30fd90189f094770d7-info.csv.gz", | |
| "buildResults/64744d6015f8f931cae0c13d1e50b092-info.csv.gz", |
vjcitn
/ cifardemo.py
Last active
February 16, 2024 10:47
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| # | |
| # 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 |
vjcitn
/ gist:da11ea5228124fd06c5e59239a54cb9d
Created
December 9, 2023 14:52
using shiny with readVcf, predictCoding, ...
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| 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), |
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| # 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))) |
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| # 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
/ check_discrepant_pkgs.R
Created
October 1, 2023 00:08
code in this gist attempts to prepare R to identify causes of CHECK_SUGGESTS_ONLY errors
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| 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", |
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