Skip to content

Instantly share code, notes, and snippets.

Avatar

Saket Choudhary saketkc

View GitHub Profile
View activate_rapids_ai.py
import sys, os
dist_package_index = sys.path.index('/usr/local/lib/python3.6/dist-packages')
sys.path = sys.path[:dist_package_index] + ['/usr/local/lib/python3.6/site-packages'] + sys.path[dist_package_index:]
sys.path
exec(open('rapidsai-csp-utils/colab/update_modules.py').read(), globals())
View CDF.ipynb
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
View riboHMM_env.yaml
name: ribohmm
channels:
- conda-forge
- bioconda
- r
- defaults
dependencies:
- bcftools=1.9=h4da6232_0
- htslib=1.9=hc238db4_4
- libdeflate=1.0=h470a237_0
@saketkc
saketkc / Pix-Plot-Demo.ipynb
Created Jul 5, 2018
Demo of Pix-plot with progress bars
View Pix-Plot-Demo.ipynb
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
View CCA--ggvegan.ipynb
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
View Knee-point.ipynb
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
@saketkc
saketkc / dotplot_barplot_goseq.R
Last active Aug 1, 2019
clusterProfiler inspiredbarplot and dotplot for GOSeq
View dotplot_barplot_goseq.R
barplot <- function(df, showCategory=15){
df <- df[with(df, order(ratio, padj, decreasing = c(TRUE, FALSE))),]
df <- head(df, n=showCategory)
breaks <- round( c(0, 1/4, 2/4, 3/4, 1) * max(df[['ratio']]) , 2)
p_plot <- ggplot(df, aes_string(x="term", y="ratio", fill="padj")) +
geom_col() +
scale_y_continuous(expand=c(0, 0), breaks=breaks, limits=c(0, max(df[["ratio"]]+0.05))) +
scale_x_discrete(name='GO term') +
scale_fill_continuous(low="#00dbde", high="#FFF94C") +
theme(text=ggplot2::element_text(size=9)) +
View Sequence logo using matplotlib.ipynb
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
View Sequence logo using matplotlib.ipynb
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
View UGC%27s+%27preferred%27+journal+%27predatory%27%3F.ipynb
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.