cgpu

FID	IID	PAT	MAT	SEX	PHE	year_of_birth	participant_ethnic_category	death_date	sars.cov.2_positive	height_hcm
10_10	10_10	0	0	2	1	25	8	20200929	2	1.65869684755143
11_11	11_11	0	0	1	0	32	8	20200929	1	2.05760365489074
13_13	13_13	0	1	2	1	8	8	20200929	1	1.91661311219814
15_15	15_15	0	1	1	0	9	8	20200929	2	1.70644503349575
21_21	21_21	0	1	2	0	26	8	20200929	2	1.68937434957125
26_26	26_26	0	1	2	0	25	8	20200929	2	1.62607132142262
40_40	40_40	0	0	2	0	31	8	20200929	2	1.98534853658691
52_52	52_52	0	1	2	0	70	8	20200929	1	1.63362615482562
53_53	53_53	0	1	1	0	11	8	20200929	2	1.84182132278676

cgpu

S1,S2,S3
ARHGEF10L,11.1818,11.0186,11.243
HIF3A,5.2482,5.3847,4.0013
RNF17,4.1956,0,0
RNF10,11.504,11.669,12.0791
RNF11,9.5995,11.398,9.8248
RNF13,9.6257,10.8249,10.5608
GTF2IP1,11.8053,11.5487,12.1228
REM1,5.6835,3.5408,3.5582
MTVR2,0,1.4714,0

cgpu

# Install nvm with node and npm
RUN curl https://raw.githubusercontent.com/creationix/nvm/v0.30.1/install.sh | bash && \
    source /home/jovyan/.nvm/nvm.sh && \
    nvm install 8.4 && \
    npm install -g yarn && \
    yarn config set ignore-engines true && \
    cd /tmp && \
    git clone https://github.com/jupyterlab/jupyterlab-monaco.git && \
    cd jupyterlab-monaco && \
    yarn install && \

cgpu

while read line
do
    srr=$line
    numLines=$(fastq-dump -X 1 -Z --split-spot $srr | wc -l)
    if [ $numLines -eq 4 ]
    then
    echo "$srr,single_end" 
    echo "$srr,single_end" >> file.log
    else
    echo "$srr,paired_end" 

cgpu

#!/usr/bin/env bash
# sra-paired.sh
# Kamil Slowikowski
# April 23, 2014
#
# Check if an SRA file contains paired-end sequencing data.
#
# See documentation for the SRA Toolkit:
# http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=fastq-dump

cgpu

cgpu

# 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,...)

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# Adding roxygen comments
#' A function for generating an interactive violin plot, and an ! interactive annotated gg violin plot
#'
#' This function generate a customisable annotated violin plot in png from a dataframe with an outcome variable with 2 levels
#' @param data dataframe with features as coluns, observations as rows. All features must continuous variables. A column denoting the case control must be present
#' @param group The column name from the column holding the case control status information
#' @param feature The column name from the feature of interest for comparison between groups
#' @param ctrl_id The value that denotes the controls in the "group" column (eg. "0", "Control"). Must be provided in double quotes
#' @param case_id The value that denotes the cases in the "group" column (eg. "1", "Case"). Must be provided in double quotes
#' @param SAVEDIR absolut path to output directory

cgpu

 cat gencode.v33.primary_assembly.annotation.gtf | awk 'BEGIN{FS="\t"}{split($9,a,";"); if($3~"gene") print a[1]"\t"a[3]"\t"$1":"$4"-"$5"\t"a[2]"\t"$7}' |sed 's/gene_id "//' | sed 's/gene_id "//' | sed 's/gene_type "//'| sed 's/gene_name "//' | sed 's/"//g' | awk 'BEGIN{FS="\t"}{split($3,a,"[:-]"); print $1"\t"$2"\t"a[1]"\t"a[2]"\t"a[3]"\t"$4"\t"$5"\t"a[3]-a[2];}' | sed "1i\Geneid\tGeneSymbol\tChromosome\tStart\tEnd\tClass\tStrand\tLength" | less -S

cgpu

            theme(text              = element_text(           color = "#4A637B", face = "bold", family = 'Helvetica')
                  ,plot.caption     = element_text(size =  9, color = "#8d99ae", face = "plain"                     ) 
                  ,plot.title       = element_text(size = 18, color = "#2b2d42", face = "bold", hjust=0.15          )
                  ,axis.text.y      = element_text(size = 10, color = "#8d99ae", face = "bold", hjust=1.1           )
                  ,axis.title.x     = element_text(size = 14 ,                                  hjust = 0.15        )
                  ,axis.text.x      = element_blank()
                  ,axis.title.y     = element_blank()
                  ,axis.ticks.x     = element_blank()
                  ,axis.ticks.y     = element_blank()
                  ,plot.margin      = unit(c(1,1,1,1),"cm")