raivivek

[...]
run_differential <- function(counts_mat, metadata,
                             design = "Disease.Status + Age + Sex + BMI",
                             min_reads_per_sample = 5,
                             min_fraction_of_sample = .25) {
  sample_ids <- colnames(counts_mat)
  message(glue("info: counts matrix: {paste(dim(counts_mat), collapse = ', ')} \t Covariate matrix: {paste(dim(metadata), collapse = ', ')}"))
  message("info: preparing colData..")
  colData <- metadata %>%
    mutate(Sample.ID = factor(Sample.ID, levels = sample_ids, ordered = T),

raivivek

git

list files in another branch

git ls-files --with-tree=another-branch

grep through all revisions of a repo

git grep -B1 -A2 AWSLambdaBasicExecutionRole $(git rev-list --all) -- *.tf

raivivek

Structure

The website is hosted from the repository scjparker.github.io. The repo has two branches:

• master where the deployed website lives
• source where the source code for the website lives

The content pushed to the master branch is automatically shown on the theparkerlab.org homepage by the GitHub.

Making changes

raivivek

"A little bit of slope makes up for a lot of y-intercept"

01/13/2012. From a lecture by Professor John Ousterhout at Stanford, class CS140

Here's today's thought for the weekend. A little bit of slope makes up for a lot of Y-intercept.

[Laughter]

raivivek

#!/usr/local/bin/python
# -*- coding: utf-8 -*-

# Usage: pandoc --filter=wayback.py input
# Install pandocfilters and requests with pip before using
# Warning: may take a while to process input with lots of links
# Note: Links that can't be saved to WBM or already point to WBM are left as is

from pandocfilters import toJSONFilter, Link
import requests

raivivek

'''''list highlights and annotations by ISBN and book:
select 
ISBN, title,
text, annotation
from bookmark
left outer join content
on (content.contentID=bookmark.VolumeID and content.ContentType=6)
where  
text is not null;

raivivek

Bedtools Cheatsheet

General:

Tools	Description
flank	Create new intervals from the flanks of existing intervals.
slop	Adjust the size of intervals.
shift	Adjust the position of intervals.
subtract	Remove intervals based on overlaps b/w two files.

raivivek

This gist contains a list of points I found very useful while watching the fast.ai "Practical deep learning for coders" and "Cutting edge deep learning for coders" MOOC by Jeremy Howard and team. This list may not be complete as I watched the video at 1.5x speed on marathon but I did write down as many things I found to be very useful to get a model working. A fair warning the points are in no particular order, you may find the topics are all jumbled up.

Before beginning, I want to thank Jeremy Howard, Rachel Thomas, and the entire fast.ai team in making this awesome practically oriented MOOC.

1. Progressive image resolution training: Train the network on lower res first and then increase the resolution to get better performance. This can be thought of as transfer learning from the same dataset but at a different resolution. There is one paper by NVIDIA as well that used such an approach to train GANs.

2. Cyclical learning rates: Gradually increasing the learning rate initially helps to avoid getting stuc

raivivek

library(ggplot2)
library(grid)
# define consistent ggplot theme to apply to all figures
theme_ms <- function(base_size=12, base_family="Helvetica") {
  library(grid)
  (theme_bw(base_size = base_size, base_family = base_family)+
      theme(text=element_text(color="black"),
            axis.title=element_text(face="bold", size = rel(1.3)),
            axis.text=element_text(size = rel(1), color = "black"),
            legend.title=element_text(face="bold"),

raivivek

Flash Asus TM-AC1900 to Asus RT-AC68U

Asus TM-AC1900 is a T-Mobile rebranded router but exactly the same hardware as a RT-AC68U. It is touted as one of the best available routers in the market and is highly rated. However, TM-AC1900 contains a T-Mobile firmware which runs several years behind the official Asus firmware available for the hardware. Thus, it is of interest to "flash" the offical firmware with a newer one.

NOTE: The router works smoothly even without flashing. Don't flash if you don't need to.

Steps

Depending on the pre-installed firmware on the CellSpot router, many instructions below may or may not work for everyone. Howevery, they worked for mine.

Files needed