rahulbhadani

import umap
import zipfile
import urllib.request
import pandas as pd
import umap
urllib.request.urlretrieve("https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2230nnn/GSM2230760/suppl/GSM2230760_human4_umifm_counts.csv.gz", 'GSM2230760_human4_umifm_counts.csv.gz')

data = pd.read_csv('GSM2230760_human4_umifm_counts.csv.gz')
data.drop(columns='Unnamed: 0', inplace=True)
data.set_index("barcode", inplace=True)

rahulbhadani

folder = "/home/ivory/VersionControl/scRNASeq/python-notebook/"
file = "FilteredCount.csv"
filepath = paste(folder, file, sep="")
csv = read.csv(filepath, sep=",", row.names = 1, header= TRUE)
mat = as.matrix(csv)

rahulbhadani

# Installing scDoc from source
install.packages("https://github.com/anlingUA/scDoc/blob/master/scDoc_0.0.0.9.tar.gz?raw=true", repo=NULL, type="source")
library(scDoc)
data(zebrafish)

# Used when estimating dropout
offsets <- as.numeric(log(colSums(zebrafish)))

# Filtering step
count <- zebrafish[rowSums(zebrafish > 5) > 4, ]

rahulbhadani

# install.packages(c("Matrix", "rhdf5", "tidyverse"))
library(Matrix)
library(rhdf5)
library(tidyverse)
library(glue)

my_h5_files <- Sys.glob(
  "path/to/cellranger-per-channel/output/*/filtered_feature_bc_matrix.h5"
)

rahulbhadani

Migrating from SVN to GitHub

This gist explains the detail of migrating from SVN to Git. I have had a significant portion of my research work, paper, and source code in Subversion (SVN) since 2015. Recently we decided to migrate everything to GitHub private repository. I am detailing the steps below in case that will be helpful.

Checkout your code from SVN

svn co https://svn.engr.arizona.edu/svn/jms/jmsgroup/trunk/wildcat wildcat_SVN

This will save the subversion code in wildcat_SVN. Run following inside wildcat_SVN directory to get the list of author information who have committed so far.

rahulbhadani

Requisite for reading rosbag files in Python

If you are interested in reading bag files in python, you will need to install bagpy package. I recommend using virtual environment for installation.

Prerequisite

1. Ubuntu
2. Python 3.6 or higher preferred, might work with other versions of python but not tested on them.

Creating virtual environment

rahulbhadani

Reading bag files in MATLAB

MATLAB provides toolbox for reading bag files in a number of ways. For MATLAB Version 2019a and beyond, ROS Toolbox is required for reading bag files. For earlier version upto 2016a, Robotic System Toolbox is required.

I have also written a high-level wrapper for reading and visualizing some widely known topics by a few API calls only. Details are described below:

Using MATLAB Toolbox to read bag files

Start MATLAB by typing matlab in the terminal if you use Linux or double click MATLAB icon if you are using windows.

rahulbhadani

Inspired by dannyfritz/commit-message-emoji

See also gitmoji.

Commit type	Emoji
Initial commit	🎉 :tada:
Version tag	🔖 :bookmark:
New feature	✨ :sparkles:
Bugfix	🐛 :bug:

rahulbhadani

def convex_hull_graham(points):
    '''
    Returns points on convex hull in CCW order according to Graham's scan algorithm. 
    By Tom Switzer <[email protected]>.
    '''
    TURN_LEFT, TURN_RIGHT, TURN_NONE = (1, -1, 0)

    def cmp(a, b):
        return (a > b) - (a < b)

rahulbhadani