Laurent Gautier lgautier
lgautier
/ agent-ai.ipynb
Created
May 14, 2025 17:26
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lgautier
/ reticulate-from-rpy2.py
Created
March 25, 2023 16:24
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| Python 3.8.10 (default, Mar 13 2023, 10:26:41) | |
| Type 'copyright', 'credits' or 'license' for more information | |
| IPython 8.11.0 -- An enhanced Interactive Python. Type '?' for help. | |
| In [1]: from rpy2.robjects.packages import importr | |
| In [2]: reticulate = importr('reticulate') | |
| WARNING: The R package "reticulate" only fixed recently | |
| an issue that caused a segfault when used with rpy2: |
lgautier
/ multiproc_lab.py
Created
January 3, 2020 23:02
"Lab" to show how to perform parallel R computing using `multiprocessing`.
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| import argparse | |
| import multiprocessing as mp | |
| import uuid | |
| import rpy2.rinterface as ri | |
| import rpy2.rinterface_lib.embedded | |
| R_ID_TAG = '_rpy2_R_id_' | |
| def print_setup(args): |
lgautier
/ rpy2-ld-library-path.sh
Created
December 31, 2019 17:55
Set LD_LIBRARY_PATH for rpy2 when R is in a non-system location
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| export LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):${LD_LIBRARY_PATH} |
lgautier
/ demo_benchmark_mashingp.sh
Last active
January 30, 2017 04:37
Demo/benchmark mashing-pumpkins to build minhash sketches
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| #!/bin/sh | |
| echo | |
| echo '---------------' | |
| echo ' test w/ FASTA ' | |
| echo '---------------' | |
| testchrom=chr1.fa.gz | |
| if [ ! -f "${testchrom}" ]; then |
lgautier
/ dplyr.ipynb
Last active
January 18, 2016 21:00
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lgautier
/ rpy2_stap_example
Last active
August 29, 2015 14:25
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| power <- function(x, n) { | |
| # a not-so-useful reimplementation | |
| x ^ n | |
| } | |
| square <- function(x) { | |
| x^2 | |
| } | |
| cube <- function(x) { |
lgautier
/ ipysetup.py
Created
December 26, 2014 16:50
Customization of rpy2 (see comments at https://bitbucket.org/rpy2/rpy2/issue/230/rmagic-specific-conversion)
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| # This is a setup snippet for an ipython notebook. | |
| # It requires the presence of variable 'setup_digest', | |
| # defined in the cell controlling the setup. | |
| if 'setup_digest' not in locals(): | |
| import rpy2 | |
| %load_ext rpy2.ipython | |
| # pigheaded / slow rpy2 developpers, | |
| # customize away: | |
| from rpy2.robjects.conversion import ri2py |
lgautier
/ rmagic_singledispatch
Last active
August 29, 2015 14:08
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| { | |
| "metadata": { | |
| "name": "", | |
| "signature": "sha256:cd75955d68d7ca272ff32886ce865002acb49b25f2e1cfba237539e70925eeda" | |
| }, | |
| "nbformat": 3, | |
| "nbformat_minor": 0, | |
| "worksheets": [ | |
| { | |
| "cells": [ |
lgautier
/ gist:955e14077322480803e2
Created
September 30, 2014 02:36
rpy2 and HTML display in ipython
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| { | |
| "metadata": { | |
| "name": "", | |
| "signature": "sha256:e814b7d85c1dc274b3c62ca6849951326dee84fa31b999f9735064f46fb45a7a" | |
| }, | |
| "nbformat": 3, | |
| "nbformat_minor": 0, | |
| "worksheets": [ | |
| { | |
| "cells": [ |
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