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bitBites (2026-02-11): Codex demo, AlphaGenome
bitBite
dplyr column recording: extension of
case_when
with cleaner coding.
Feb 11, 2026
3 min
bitBites (2026-02-04): R AI tool tutorials, single cell research and a spatial signal correction tool
bitBite
This week’s recap spans new project-based tutorials in the R AI ecosystem, reflections on how coding agents reshape learning, and recent advances in computational biology. I…
Feb 4, 2026
4 min
bitBites (2026-01-28): Posit Recap, EcoTyper and H&E to proteomics
bitBite
This week we will recap Posit summary of 2025, Claude-assisted refactoring stories, a few bioinformatics relevant new R packages, and some exciting work predicting spatial…
Jan 28, 2026
5 min
bitBites (2026-01-21): TMLE, Claude skills, Stack
bitBite
Targeted Maximum Likelihood Estimation (TMLE)
is a semiparametric causal inference method for estimating the
average treatment effect (ATE)
. It yield consistent ATE…
Jan 21, 2026
6 min
bitBites (2026-01-14): single-cell for drug development and clinical translation, R+Python polyglot, claude code
bitBite
In this week’s bitBits, I will highlight recent advances in using single-cell transcriptomics for drug prioritization and clinical translation, including frameworks like…
Jan 14, 2026
7 min
bitBites (2026-01-07): R stats, LLM prompts and update, Virtual cell
bitBite
R Package Development Advent Calendar 2025 by Athanasia Mo Mowinckel offers a comprehensive journey through R package development. Even with prior experience, I still…
Jan 7, 2026
7 min
bitBites (2026-01-01): LLM shiny, Advert of Agent, FOCUS, Scalable Perturb-seq
bitBite
Inspired by Stephen Turner
1
’s weekly recap series, I’m starting a series called bitBites to regularly review what I read and learn. This is part of my New Year’s…
Jan 1, 2026
5 min
Python Environment Manager - uv
Python
Bash
As a computational biologist, I have relied on conda for Python package management for over a decade. This is largely because most bioinformatics packages and software are…
Dec 21, 2025
12 min
Buy low sell high on big tech stocks?
R
tidyTuesday
I am interested in Big Tech Stock Prices since I personally hold several big Tech stocks and experienced bloody plummeting in the last year. As an amateur investor, I have…
Feb 18, 2023
32 min
Understanding survival analysis - part 1
statistics
R
bioinformatics
I have been performing survival analysis for a while. Although I can create standard survival curves and summarize hypothesis testing tables, I have never really
UNDERSTOOD
i…
Jan 16, 2023
10 min
TidyTuesday: Open Psychometrics 2022Wk33
MacOS
R
TidyTuesday 2022-08-16
Nov 2, 2022
3 min
Install multiple versions of R in MacOS
MacOS
R
Whenever there is new release of R at CRAN, I am always tempted to install the new version so that I can use the fancy new tools. However, switch to new version of R is…
Oct 31, 2022
3 min
Use API in R and solve common errors
R
API
An API (Application Programming Interface) is an intermediary between a large dataset and the applications at user end. It provides an accessible way to request data from a…
Oct 26, 2022
4 min
Interpreting the coefficients of Generalized Linear Model
R
GLM
tidymodels
Linear model is the most popular model used in various of fields, due to its simple execution and interpretation. It can be not only used to predict like all other machine…
Feb 28, 2022
13 min
TidyTuesday: predict chocolate rating with xgboost
R
tidyTuesday
tidymodels
Load required libraries
Jan 23, 2022
9 min
TidyTuesday: predict ultra race time
R
tidyTuesday
tidymodels
Load required libraries
Nov 2, 2021
8 min
Taking options from command line
R
bash
perl
Taking in options from command line is an essential step towards generalized usage of scripts. However, it is a chapter I skipped in almost all language textbooks since my…
Aug 22, 2020
22 min
Transition from dplyr to data.table
R
data wrangle
dplyr
and
tidyr
have totally changed the way we code in R. I particularly love the pipe
%>%
which comes from
magrittr
package and makes the code easy to read and understand.…
Jun 25, 2020
6 min
ML pipeline with tidymodels vs. caret
R
ML
tidymodels
As a DS beginner, I first came across ML in R by studying the book Hands-On Machine Learning with R. The book mainly focuses on the package
caret
with general introductions…
Apr 30, 2020
13 min
External persistent data I/O using ShinyApp
R
shiny
Shiny App is a fantastic application in Rstudio and makes the data processing more accessible (and fun!). Most easy shiny apps are made to represent data based on a given…
Mar 30, 2020
33 min
All about git
bash
git
Recently I have actively participated two team projects (PAWS and 2020datahack) which involves multiple team members and a lot of group decisions. For the first time, I…
Feb 11, 2020
9 min
Network visualization - Part 3
R
network
visualization
In the previous two posts, we discussed about IGRAPH object and how to manipulate, measure and cluster it. In this final post of network analysis series, I will focus on the…
Sep 4, 2019
8 min
Network Analysis in R - Part 2
R
network
In last post, I covered the basic components of IGRAPH objects and how to manipulate IGRAPH. You may notice that most of those manipulation do not really require a IGRAPH…
Aug 24, 2019
5 min
Network Analysis in R - Part 1
R
network
Network analysis, also called graph analysis, is to study the complexity of the inter-relationships between actors of all sorts and provides an architectural view of…
Jul 11, 2019
10 min
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