mblondel

# Mathieu Blondel, February 2012
# License: BSD 3 clause

# Port to Python of examples in chapter 5 of
# "Introductory Statistics with R" by Peter Dalgaard

import numpy as np
from scipy.stats import ttest_1samp, wilcoxon, ttest_ind, mannwhitneyu

# daily intake of energy in kJ for 11 women

stephenturner

## RNA-seq analysis with DESeq2
## Stephen Turner, @genetics_blog

# RNA-seq data from GSE52202
# http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse52202. All patients with
# ALS, 4 with C9 expansion ("exp"), 4 controls without expansion ("ctl")

# Import & pre-process ----------------------------------------------------

# Import data from featureCounts

shenwei356

Filtering Spades assembly result according to coverage information in sequence header

Sample sequence

$ cat contigs.fasta 
>NODE_1_length_869844_cov_1135.34
ACTGNacgtn 
>NODE_2_length_576386_cov_975.882
acgtn

nicolasdao

Exhaustive list of SPDX (Software Package Data Exchange) licenses: https://spdx.org/licenses/

Table of Contents

• TL;DR - The BSD 3 Clause License Should Do
• In a Nutshell
• 3 Main Types of Open Source Licenses
  • 1. MIT
  • 2. Apache
  • 3. GPL
• The BSD License Case

lwaldron

metaphlanToPhyloseq <- function(
  metaphlandir,
  metadat=NULL,
  simplify=TRUE){
  ## tax is a matrix or data.frame with the table of taxonomic abundances, rows are taxa, columns are samples
  ## metadat is an optional data.frame of specimen metadata, rows are samples, columns are variables
  ## if simplify=TRUE, use only the most detailed level of taxa names in the final object
  ## metaphlanToPhyloseq("~/Downloads/metaphlan_bugs_list")
  .getMetaphlanTree <- function(removeGCF=TRUE, simplify=TRUE){
    if (!requireNamespace("ape")) {

zorbax

#!/bin/bash
usage ()
{
    echo ""
    echo "Usage : `basename $0` <tableL6.txt> <L6_clean.tsv>"
    echo ""
    exit
}

if [ "$1" = "" ]; then

zorbax

( conda create -y -n "melonpann" && source activate "melonpann" && \
  conda install r-base=3.5.0 r-devtools r-fbasics -yc r && \
  R -q -e "install.packages('BiocManager', repos='http://cran.r-project.org'); \
           library('BiocManager'); BiocManager::install('ccrepe');" && \
  R -q -e "install.packages('optparse', repos='http://cran.r-project.org')" && \
  R -q -e "install.packages('AssocTests', repos='http://cran.r-project.org')" && \
  R -q -e "install.packages('glmnet', repos='http://cran.r-project.org')" && \
  R -q -e "install.packages('HDtweedie', repos='http://cran.r-project.org')" && \
  R -q -e "install.packages('getopt', repos='http://cran.r-project.org')" && \
  R -q -e "install.packages('doParallel', repos='http://cran.r-project.org')" && \