crazyhottommy

---
title: "02_bioc_curated_TCGA_data"
author: "Ming Tang"
date: "November 9, 2017"
output: html_document
---

```{r}
devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")
library(here)

crazyhottommy

#!/bin/bash
# function Extract for common file formats

function extract {
 if [ -z "$1" ]; then
    # display usage if no parameters given
    echo "Usage: extract <path/file_name>.<zip|rar|bz2|gz|tar|tbz2|tgz|Z|7z|xz|ex|tar.bz2|tar.gz|tar.xz>"
 else
    if [ -f "$1" ] ; then
        NAME=${1%.*}

crazyhottommy

crazyhottommy

```{r}
library(GEOquery)
library(tidyverse)

meta<- getGEO(GEO= "GSE185507",GSEMatrix=FALSE)
```

```{r}
meta@gsms$GSM5616943@header$characteristics_ch1
```

crazyhottommy

```{r}

TAAs<- c("MSLN", "EGFR", "ERBB2", "CEACAM5", "NECTIN4", "EPCAM", "MUC16", "MUC1", "CD276",
         "FOLH1", "DLL3", "VTCN1", "PROM1", "PVR", "CLDN6", "MET", "FOLR1", "TNFRSF10B", "TACSTD2")
```

```{r}
TCGAExprsAndPheno2 <- function(gene_vector, cancer_types = "all", expression_type = "TPM"){
  library(recount3)
  ## Get all possible projects

crazyhottommy

## get all the promoter sequences for human hg19 genome
## Author: Ming Tang (Tommy)
## Date: 04/30/2015

## load the libraries 
library(GenomicRanges)
library(BSgenome.Hsapiens.UCSC.hg19)
BSgenome.Hsapiens.UCSC.hg19
# or
Hsapiens

crazyhottommy

I use sshfs to mount remote servers. but I also want to connecting windows servers to my ubuntu.

If there's one good thing that I can say about Windows XP is that it supports the SMB protocol. This enables a computer running Windows to share files, folders, and more with another PC. All that other PC needs is the right software to take advantage of the SMB protocol. Luckily, that software is available for GNU/Linux.

on mac, I can click the Finder bar --->Go---> Connect to Server and then type in the address.

crazyhottommy

> library(dplyr)

> cars %>% 
  as_tibble %>% 
  mutate(case_code = case_when(
                              speed == 4 & dist == 2 ~ "this",
                              dist > 6 & dist == 10 ~ "is",
                              speed >=10 & dist >= 18 ~ "awesome"))
                   
 # A tibble: 50 × 3

crazyhottommy

other databases: https://twitter.com/tangming2005/status/1470513427080699905

GSEA has a geneset https://www.gsea-msigdb.org/gsea/msigdb/cards/GOCC_CELL_SURFACE.html use https://cran.r-project.org/web/packages/msigdbr/vignettes/msigdbr-intro.html to get it

library(msigdbr)
cell_surface_proteins<- msigdbr(species = "Homo sapiens", category = "C5") %>% 
  filter(gs_name == "GOCC_CELL_SURFACE") %>%
 pull(human_gene_symbol)

crazyhottommy

backup dotfiles

• Following will copy all of dot ~/. files and directories (including its contents) directly underneath home directory.
• To avoid copying cache and other local configs, e.g., that of web browser, java apps, etc., preferably query directory size tool under entire home $HOME/, using ncdu $HOME of similar tool.
• Exclude all those large directories using rsync --exclude=.local --exclude=.cache format
• Avoid rsync password, ssh keys, .bash_history, etc. if you are uploading to github, etc.
• rsync home dotfiles and configs as follows:

# in your local machine