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Nitesh Turaga nturaga

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@nturaga
nturaga / issues.md
Created January 10, 2024 00:18 
❯ checking R code for possible problems ... [11s/10s] NOTE
  .filter_transciptome: no visible binding for global variable
    'tempus_ensembl_id'
  .filter_transciptome: no visible binding for global variable
    'gene_symbol'
  .tbl_cnv: no visible binding for global variable 'n_reads'
  .tbl_cnv: no visible global function definition for 'STRING_AGG'
  .tbl_diagnosis: no visible global function definition for 'date_diff'
  .tbl_diagnosis_dates: no visible binding for global variable
@nturaga
nturaga / text_files.txt
Created October 12, 2023 15:23
Write a R package vignette for a package called "Tempustables" that has the following functions with descriptions and examples as given below. The vignette needs to be fairly easy for users to follow. Provide examples and description for each function.
Collect Normalized RNA by Cohort
Description:
Collecting the whole transcriptome for over 100 samples from
'normalized_rna' in your R session will typically fail, requiring
you to write some sort of a loop to get all the patients. This
function does all that work for you and runs the query in
parallel.
@nturaga
nturaga / patch.patch
Created September 8, 2023 17:55
diff --cc R/tbl_patient_record.R
index 43600b0,b236cb4..0000000
--- a/R/tbl_patient_record.R
+++ b/R/tbl_patient_record.R
@@@ -1,132 -1,154 +1,198 @@@
-#' Table of patient records with a curated diagnosis
+#' Return a Table of Patient Records with a Curated Diagnosis
#'
-#' Returns relevant metadata regarding the patient records and the
-#' depth of associated data for each record. Excludes records that are
@nturaga
nturaga / tmp.txt
Created August 7, 2023 18:57
tbl_patient_record.R
44: tbl("patient") |>
61: tbl("molecular_inventory") |>
70: tbl("combined_diagnosis") |>
83: tbl("medications_enhanced") |>
tbl_sample_therapy.R
57: tbl("onco_care_plan") |>
@nturaga
nturaga / how_to_investigate_docker_image.md
Created July 27, 2023 17:08

How to locally run the docker image

Build a new docker image

docker build -t us.gcr.io/tl-jvu4eyij9cslnrj0msep/trreports:0.0.3

Test the docker image locally

@nturaga
nturaga / tsci_gcloud.R
Created November 21, 2022 20:07
library(readr)
library(dplyr)
cmd <- 'gcloud compute instances list --filter="tn-pytorch" --format="table(name, status, labels.created_by.list(), labels.image.list())" > tsci_gcloud.csv'
system(cmd)
dat <- read_table('tsci_gcloud.csv')
@nturaga
nturaga / review_template.md
Created August 22, 2022 13:18

Review

DESCRIPTION

NAMESPACE

NEWS

R

@nturaga
nturaga / martin_cloud.R
Created August 13, 2022 11:01
setGeneric("cloud_cp", function(x, ...) standardGeneric("cloud_cp"))
cloud_rm <- function(x, ...)
UseMethod("cloud_rm")
cloud_rsync <- function(x, ...)
UseMethod("cloud_rsync")
## azure
setClass("Cloud")
AzureCloud <- setClass("AzureCloud", contains = "Cloud")
setMethod("cloud_cp", "AzureCloud", function(x, from, to, ...) {
## implement cp for Azure
@nturaga
nturaga / anvil_repo_stats.txt
Created June 7, 2022 13:36
> AnVIL:::repository_stats()
Container: bioconductor_docker
Bioconductor version: 3.15
Bioconductor binary repos:
https://bioconductor.org/packages/3.15/container-binaries/bioconductor_docker
PACKAGES timestamp: 2022-05-31 13:51:00 UTC
Query timestamp: 2022-06-07 13:25 UTC
Bioconductor software packages: 2120
Binary packages: 3692
Binary software packages: 2100
@nturaga
nturaga / branch_rename.sh
Created May 27, 2022 17:24
git pull origin master
git pull upstream master
## Make sure devel does not already exist
git branch -d devel
## Create and push the devel branch
git checkout -b devel
git push origin devel