View umap.R
#install UMAP from https://github.com/lmcinnes/umap
#install.packages("rPython")
umap <- function(x,n_neighbors=10,min_dist=0.1,metric="euclidean"){
x <- as.matrix(x)
colnames(x) <- NULL
rPython::python.exec( c( "def umap(data,n,mdist,metric):",
"\timport umap" ,
"\timport numpy",
"\tembedding = umap.UMAP(n_neighbors=n,min_dist=mdist,metric=metric).fit_transform(data)",
View clinical_data_TCGA.md
library('TCGAbiolinks')
library('plyr')
library('devtools')

projects<- "TCGA-LUAD"

clin <- lapply(projects, function(p) {
View mouse2hum_biomart_ens87.txt
This file has been truncated, but you can view the full file.
Gene ID Transcript ID Human associated gene name Human gene stable ID Associated Gene Name
ENSMUSG00000064336 ENSMUST00000082387 mt-Tf
ENSMUSG00000064337 ENSMUST00000082388 mt-Rnr1
ENSMUSG00000064338 ENSMUST00000082389 mt-Tv
ENSMUSG00000064339 ENSMUST00000082390 mt-Rnr2
ENSMUSG00000064340 ENSMUST00000082391 mt-Tl1
ENSMUSG00000064341 ENSMUST00000082392 MT-ND1 ENSG00000198888 mt-Nd1
ENSMUSG00000064342 ENSMUST00000082393 mt-Ti
ENSMUSG00000064343 ENSMUST00000082394 mt-Tq
View convert_msigdb_human_gmt_to_mouse.md
View call_peaks.sh
#! /bin/bash
set -e
set -u
set -o pipefail
root=`pwd`
mkdir macs14_pbs
cat bam_names.txt | while read -r IP Input
View convert_UUID_to_TCGA_barcode.md
View recursive_merge_bedpe.md
View generate_TPM_TCGA.rmd
title author date output
02_bioc_curated_TCGA_data
Ming Tang
November 9, 2017
html_document
devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")
library(here)
View mp_primer_v2.sh
#!/bin/bash
printf "\n *** BIS BATCH PRIMER version 2.0 ***"
printf "\n\n !!! 'Primer3 & fastx-toolkit' must be installed on the system.\n\n !!! Edit parameters (e.g. sizes, Tm, and etc) before start\n\n "
printf "\n\n Usage : \n ./mp_primer.sh FASTA PARAMETER \n\n"
printf " >>> input FASTA = "$1
printf " \n >>> parameters = "$2
printf "\n\n\n ()()() Running... \n\n"
if [ -f $1 -a -f $2 ]; then
View create_R.3.3.2_conda_env.md
ssh mdaris337
conda create -n R330

source activate R330

conda install -c r r=3.3.2 r-essentials