mukhortov

Migrate GitHub issues with comments and labels to Jira

Set up the environment

1. Instal Deno. It's a secure runtime for JavaScript and TypeScript.
2. Generate a personal access token for GitHub. And save it to ~/.github-oauth. You can use the following command to save it:

   echo generated_github_personal_access_token_goes_here > ~/.github-oauth

djnavarro

library(flametree)
library(ggplot2)
library(gganimate)

dat <- flametree_grow(time = 13)

pic <- ggplot(
  data = dat,
  mapping = aes(
    x = coord_x,

lindenb

params.directories="."
params.headsize=100000
params.extensions="bam bai"
params.help=false
params.extrafind=""
params.lines = 1000
params.publishDir="."

def helpMessage() {
  log.info"""

GabrielSGoncalves

import papermill as pm

pm.execute_notebook('weather_forecast_using_pyowm.ipynb',
                    'weather_forecast_using_pyowm_output.ipynb',
                    parameters={'city':'Sao Paulo,BR'},
                    kernel_name='papermill-tutorial')

cgpu

#' Create a Kaplan-Meier plot using ggplot2
#'
#' @param sfit: a survfit object
#' @param table: logical: Create a table graphic below the K-M plot, indicating at-risk numbers?
#' @param returns logical: if TRUE, return an arrangeGrob object
#' @param xlabs: x-axis label
#' @param ylabs: y-axis label
#' @param ystratalabs: The strata labels. Default = levels(summary(sfit)$strata)
#' @param ystrataname: The legend name. Default = "Strata"
#' @param timeby numeric: control the granularity along the time-axis

cgpu

ggroc <- function(roc, showAUC = TRUE, interval = 0.2, breaks = seq(0, 1, interval)){
  require(pROC)
  if(class(roc) != "roc")
    simpleError("Please provide roc object from pROC package")
  plotx <- rev(roc$specificities)
  ploty <- rev(roc$sensitivities)
  
  ggplot(NULL, aes(x = plotx, y = ploty)) +
    geom_segment(aes(x = 0, y = 1, xend = 1,yend = 0), alpha = 0.5) + 
    geom_step() +

npearce

UPDATE (March 2020, thanks @ic): I don't know the exact AMI version but yum install docker now works on the latest Amazon Linux 2. The instructions below may still be relevant depending on the vintage AMI you are using.

Amazon changed the install in Linux 2. One no-longer using 'yum' See: https://aws.amazon.com/amazon-linux-2/release-notes/

Docker CE Install

sudo amazon-linux-extras install docker
sudo service docker start

apreshill

# stack overflow answer from Joran Ellis:
# http://stackoverflow.com/questions/5319839/read-multiple-csv-files-into-separate-data-frames

# If the path is different than your working directory
# you'll need to set full.names = TRUE to get the full
# paths.
my_files <- list.files("path/to/files")

# Further arguments to read.csv can be passed in ...
all_csv <- lapply(my_files,read.csv,...)

obenshaindw

#GATK Method <- Slower and keeps original ID plut dbSNP rsID
# R=Reference FASTA
# V=VCF file to add IDs to
# --dbsnp = dbsnp VCF -- download from NCBI FTP

java -jar GenomeAnalysisTK.jar -R /reference/Homo_sapiens_assembly19.fasta -T VariantAnnotator -V vcf_to_add_id_to.vcf --dbsnp /reference/dbsnp_137.b37.vcf.gz --out /data/Broad.chr1.annotated.vcf

#bcftools Method <- Faster, replaces existing ID with dbSNP rsID
/usr/bin/htslib/bcftools/bcftools annotate -a /reference/dbsnp_137.b37.vcf.gz -c ID vcf_to_add_id_to.vcf

rxaviers

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