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View CDF.ipynb
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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
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View CCA--ggvegan.ipynb
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View Knee-point.ipynb
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@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
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View Sequence logo using matplotlib.ipynb
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View UGC%27s+%27preferred%27+journal+%27predatory%27%3F.ipynb
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@saketkc
saketkc / journal_overlap.py
Created Jan 22, 2017
Find overlap between Beall's list and UGC approved list of journals
View journal_overlap.py
import pandas as pd
from operator import itemgetter
from fuzzywuzzy import fuzz
from fuzzywuzzy import process
beall_df = pd.read_csv('Beall_list.txt', header=None, sep='\t', names=['names'])
j1_df = pd.read_csv('J1.csv', header=None, names=['names'])
j2_df = pd.read_csv('J2.csv', header=None, names=['names'])
j3_df = pd.read_csv('J3.csv', header=None, names=['names'])
j4_df = pd.read_csv('J4.csv', header=None, names=['names'])
j5_df = pd.read_csv('J5.csv', header=None, names=['names'])
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