k3yavi

import requests
import argparse
import pprint
import os

def do_upload(args):
    ACCESS_TOKEN = args.token
    depid = args.deposition_id
    url = 'https://zenodo.org/api/deposit/depositions/{}'.format(depid)
    r = requests.get(url, params={'access_token': ACCESS_TOKEN})

k3yavi

k3yavi

library(Biostrings)
library(BSgenome)
library(eisaR)
library(GenomicFeatures)
library(SummarizedExperiment)
library(tximeta)
library(rjson)
library(reticulate)
library(SingleCellExperiment)
library(scater)

k3yavi

Keybase proof

I hereby claim:

• I am k3yavi on github.
• I am k3yavi (https://keybase.io/k3yavi) on keybase.
• I have a public key ASBa3ubEhE7OFhiRP-ivU-tpBGLXhbTUDAkZsbJPfu4eFQo

To claim this, I am signing this object:

k3yavi

suppressPackageStartupMessages({
  library(Signac)
  library(Seurat)
  library(Matrix)
  library(ggplot2)
  library(patchwork)
  library(dplyr)
  library(RcppRoll)
  library(fastmatch)
  library(EnsDb.Hsapiens.v86)

k3yavi

suppressPackageStartupMessages({
  library(devtools)
  library(Signac)
  library(Seurat)
  library(Matrix)
  library(ggplot2)
  library(patchwork)
  library(future)
  library(dplyr)
  library(pbapply)

k3yavi

# get the data as per https://www.cedricscherer.com/2019/05/17/the-evolution-of-a-ggplot-ep.-1/#code
library(tidyverse)
devtools::source_gist("https://gist.github.com/Z3tt/301bb0c7e3565111770121af2bd60c11")

# convert to data.frame, attach and sort region
df <- as.data.frame(df_ratios)
attach(df)

# get rid of NAs
df <- df[ ! is.na(student_ratio),]

k3yavi

#include <Rcpp.h>
using namespace Rcpp;

// This is a simple example of exporting a C++ function to R. You can
// source this function into an R session using the Rcpp::sourceCpp 
// function (or via the Source button on the editor toolbar). Learn
// more about Rcpp at:
//
//   http://www.rcpp.org/
//   http://adv-r.had.co.nz/Rcpp.html

k3yavi

from __future__ import print_function
import sys

# from https://github.com/lh3/readfq/blob/master/readfq.py
def readfq(fp): # this is a generator function
    last = None # this is a buffer keeping the last unprocessed line
    while True: # mimic closure; is it a bad idea?
        if not last: # the first record or a record following a fastq
            for l in fp: # search for the start of the next record
                if l[0] in '>@': # fasta/q header line

k3yavi

library(Seurat)
library(Signac)
library(jsonlite)

tissue_map <- c("2305121", "2305122", "2305123", "2305124", 
                "V4-A", "V4-B", "V4-C", "V4-D")
names(tissue_map) <- c(2305121, 2305122, 2305123, 2305124, seq(456, 459))
cells <- read.table("/brahms/srivastavaa/chao/visium/visium-v1.txt")$V1

coordinates <- read.table("/brahms/srivastavaa/chao/visium/visium-v1_coordinates.txt")