Vince Carey vjcitn
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| #' explore workspace tables | |
| #' @import AnVIL | |
| #' @import shiny | |
| #' @import DT | |
| #' @export | |
| tabview = function() { | |
| knownTabs = c("anvil_biosample", "donor", "project", "anvil_project", "file", | |
| "anvil_file", "activity", "anvil_activity") | |
| colhelper = list(anvil_project = c("import:timestamp", "title", |
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| make[4]: Leaving directory '/home/stvjc/SECURE/R-46-sec-src/src/extra/tre' | |
| make[4]: Entering directory '/home/stvjc/SECURE/R-46-sec-src/src/extra/tre' | |
| gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -Wall -Wformat=2 -Wconversion -Werror=format-security -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -D_GLIBCXX_ASSERTIONS -fstack-clash-protection -fstack-protector-strong -Wl,-z,nodlopen -Wl,-z,noexecstack -Wl,-z,now -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -fvisibility=hidden -c regcomp.c -o regcomp.o | |
| gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -Wall -Wformat=2 -Wconversion -Werror=format-security -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -D_GLIBCXX_ASSERTIONS -fstack-clash-protection -fstack-protector-strong -Wl,-z,nodlopen -Wl,-z,noexecstack -Wl,-z,now -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -fvisibility=hidden -c regerror.c -o regerror.o | |
| regcomp.c: In function ‘tre |
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| make[1]: Entering directory '/home/stvjc/SECURE/R-46-sec-src/doc/manual' | |
| creating RESOURCES | |
| creating FAQ | |
| creating doc/html/resources.html | |
| make[1]: Leaving directory '/home/stvjc/SECURE/R-46-sec-src/doc/manual' | |
| make[1]: Entering directory '/home/stvjc/SECURE/R-46-sec-src/m4' | |
| make[1]: Nothing to be done for 'R'. | |
| make[1]: Leaving directory '/home/stvjc/SECURE/R-46-sec-src/m4' | |
| make[1]: Entering directory '/home/stvjc/SECURE/R-46-sec-src/tools' | |
| make[1]: Nothing to be done for 'R'. |
vjcitn
/ Dockerfile.RbowtieCuda.rbocud0.0.3
Created
March 22, 2025 03:06
A dockerfile supporting a test of RbowtieCuda
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| FROM rocker/r-ver:devel | |
| RUN apt update | |
| RUN apt install -y vim git cmake | |
| RUN git clone https://github.com/FranckRICHARD01/RbowtieCuda | |
| # likely unnecessary | |
| #RUN apt-get purge -y nvidia* libnvidia* | |
| #RUN apt-get remove -y nvidia-* | |
| #RUN rm -f /etc/apt/sources.list.d/*cuda* |
vjcitn
/ gist:7580b425341eab756fd62b59d10faae7
Created
March 8, 2025 23:22
pull lung samples from atlas
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| library(cellNexus) | |
| library(dplyr) | |
| md = get_metadata() | |
| dd = md |> filter(disease=="normal", tissue %in% c("lung", "lung_parenchyma", "lung_epithelium")) | |
| lungsce1M = get_single_cell_experiment(dd) | |
| HDF5Array::setAutoBlockSize(size = 1e+09) |
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| exploreCN = function() { | |
| md = cellNexus::get_metadata() | |
| vbls = colnames(md) | |
| ui = fluidPage( | |
| sidebarLayout( | |
| sidebarPanel( | |
| helpText("navigate metadata of cellNexus"), | |
| checkboxGroupInput("vars", "vbls", | |
| choices=sort(colnames(md)), inline=TRUE) | |
| ), |
vjcitn
/ exploreCAQ.R
Created
March 7, 2025 23:00
simple descriptive data interactively filtered, for CuratedAtlasQueryR
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| library(shiny) | |
| library(CuratedAtlasQueryR) | |
| library(dplyr) | |
| library(rlang) | |
| library(DT) | |
| #' explore the CuratedAtlasQueryR metadata | |
| #' @export | |
| exploreCAQ = function() { | |
| md = CuratedAtlasQueryR::get_metadata() | |
| vbls = colnames(md) |
vjcitn
/ gist:4e6af8b67103e78d599b104b091c0abe
Created
March 2, 2025 11:13
AnnotationPipeline step -- from preliminary sqlite to sanctionedSqlite for a single organism
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| # This function can be run in a 'newPkgs' folder after sufficient | |
| # results have been obtained in annosrc/db, to produce a sanctionedSqlite database | |
| # for a single organism | |
| # the following constants are crucial | |
| whattype <- tolower("OrgDb") | |
| wheretoput <- 20250301 | |
| theversion <- "3.21.0" |
vjcitn
/ chkInclusion.R
Created
February 16, 2025 22:18
extraction of shapes and counts of transcripts within shape boundaries
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| library(SpatialData) | |
| library(SpatialData.data) | |
| library(sf) | |
| library(SummarizedExperiment) | |
| if (!exists("mb")) mb = MouseBrainMERFISH() | |
| make_circles = function(spd, shapetype="cells") { | |
| cshape = SpatialData::shapes(spd)[[shapetype]] | |
| df1 = data(cshape) |> as.data.frame() |
vjcitn
/ gist:c2a7d034b84cfc33ee1e9e3b1f9354c7
Created
February 16, 2025 18:58
code for producing sf ellipse geometry from data frame with center, lengths of major/minor radii, and orientation angle in degrees
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| df2ellipses = function(datf, npts=100) { | |
| requireNamespace("sfdep") | |
| requireNamespace("sf") | |
| stopifnot(all(c("X_centroid", "Y_centroid", "maj", "min", "angdeg") %in% names(datf))) | |
| dd = data.matrix(datf[,c("X_centroid", "Y_centroid")]) | |
| cens = lapply(seq_len(nrow(datf)), function(x) sf::st_point(dd[x,])) | |
| maj = datf$maj | |
| min = datf$min | |
| angle_in_deg = datf$angdeg # angle_in_rad/0.01745329 | |
| dd = data.matrix(cbind(dd, angdeg=datf[,"angdeg"])) #angle_in_deg) |
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