Archive

Every post I’ve written since 2013, newest first. The older ones started life on my first blog, crazyhottommy.blogspot.com, and now live here too.

2026 · 2025 · 2024 · 2023 · 2022 · 2021 · 2020 · 2019 · 2018 · 2017 · 2016 · 2015 · 2014 · 2013

2026 4 posts

Aug 17 AI in Drug Discovery: Data Quality, Not Quantity, Is the Bottleneck

May 22 Batch Effect: To Correct or Not for Bulk RNA-seq Data

Apr 24 Has AI Changed the Course of Drug Development? Three Years Later

Apr 6 I Built a Personal AI Assistant on a Mac Mini

2025 16 posts

Nov 9 Reviving BETA for Python 3: Integrating ChIP-seq and RNA-seq to Predict TF Targets

Oct 29 Understanding prcomp() center and scale Arguments for Single-Cell RNA-seq PCA

Sep 23 Do not repeat yourself: List column to do RNAseq differential expression analysis

Aug 17 Reproducible Computing in Bioinformatics: Lessons from My Latest Talk

Jul 15 How to create a GenomicRanges object in Bioconductor using canonical transcripts

Jul 4 Mastering Bioinformatics in the Age of AI: Foundational Skills for the Modern Scientist

Jun 20 How Cancer Drugs Really Work

May 22 How to calculate partial correlation controlling cancer types

May 17 Multi-Omics Integration Strategy and Deep Diving into MOFA2

May 3 Exploring Spatial Transcriptomics A Dive into Visium Data Analysis in Python

Mar 2 How I Would Learn Bioinformatics From Scratch 12 Years Later: A Roadmap

Feb 7 PCA analysis on TCGA bulk RNAseq data continued

Feb 2 PCA analysis on scATACseq data

Jan 29 PCA analysis on TCGA bulk RNAseq data

Jan 3 Biotech Data Strategy: Building a Scalable Foundation for Startups

Jan 1 Review 2024

2024 21 posts

Oct 27 I regret not doing so

Oct 19 How CCA alignment and cell label transfer work in Seurat

Oct 17 How PCA projection and cell label transfer work in Seurat

Sep 21 You need to master it if you deal with genomics data

Aug 26 A docker image to keep this site alive

Aug 19 The Most Common Mistake In Bioinformatics, one-off error

Aug 13 The Most Common Stupid Mistakes In Bioinformatics

Jun 6 Six tips to build a strong Bioinformatics CV

Jun 5 R or Python for Bioinformatics?

May 17 How to level up Real-life bioinformatics skill: from dealing with one sample to a lot of samples

May 15 Common mistakes when analyzing single-cell RNAseq data

May 9 How to separate a comma delimited string into multiple lines in R and python

May 7 S3 and S4 objects in R explained

Mar 27 Bioinformatics is not (just) statistics

Mar 20 Fine tune the best clustering resolution for scRNAseq data: trying out callback

Mar 18 Downstream of bulk RNAseq: read in salmon output using tximport and then DESeq2

Mar 13 How to preprocess GEO bulk RNAseq data with salmon

Mar 5 Do you really understand log2Fold change in single-cell RNAseq data?

Feb 23 Hidden skills beyond programming for computational biology

Jan 16 How to make a multi-group dotplot for single-cell RNAseq data

Jan 4 Great Things Take Time: How Decades of Effort Led to My Dream Career

2023 39 posts

Dec 31 Review 2023

Dec 18 Part 4 CITE-seq normalization using empty droplets with the dsb package

Dec 11 Part 3 Centered log ratio (CLR) normalization for CITE-seq protein count data

Dec 5 Part 2 CITE-seq downstream analysis: From Alevin output to Seurat visualization

Dec 3 Part 1 How to use Salmon/Alevin to preprocess CITE-seq data

Nov 15 My take on Data Challenges in Immuno-oncology, the Role of the Cloud, and Growing a Computational Biology Team

Nov 6 How to use random forest as a clustering method

Oct 31 My 4-steps to learn deep learning for genomics

Oct 26 How to convert raw counts to TPM for TCGA data and make a heatmap across cancer types

Oct 18 How to code a variational autoencoder (VAE) in R using the MNIST dataset

Oct 3 Predict TCR cancer specificity using 1d convolutional and LSTM neural networks

Sep 28 How to create pseudobulk from single-cell RNAseq data

Sep 24 Generative AI: Text generation using Long short-term memory (LSTM) model

Sep 11 Omics Playground: Derive biological insights from your omics data at your fingertip

Sep 9 How to use 1d convolutional neural network (conv1d) to predict DNA sequence binding to protein

Sep 3 Long Short-term memory (LSTM) Recurrent Neural Network (RNN) to classify movie reviews

Aug 31 Understand word embedding and use deep learning to classify movie reviews

Aug 22 multi-omics data integration: a case study with transcriptomics and genomics mutation data

Aug 8 neighborhood/cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor

Jul 23 scRNAseq clustering significance test: an unsolvable problem?

Jul 15 Navigating Variant Calling for Disease-Causing Mutations: The state-of-art process

Jul 14 Reuse the single cell data! How to create a seurat object from GEO datasets

Jul 13 10 single-cell data benchmarking papers

Jun 15 Has AI changed the course of Drug Development?

Jun 8 How to add boxplots or density plots side-by-side a scatterplot: a single cell case study

Jun 7 Unlock the Power of Genomics Data Analysis: Watershed's Seamless Cloud Computing Solution

Apr 14 How to do neighborhood/cellular niches analysis with spatial transcriptome data

Apr 9 How to classify MNIST images with convolutional neural network

Mar 30 How to construct a spatial object in Seurat

Mar 24 Deep learning to predict cancer from healthy controls using TCRseq data

Mar 18 Basic tensor/array manipulations in R

Mar 11 Deep learning with Keras using MNIST dataset

Mar 5 How to deal with overplotting without being fooled

Feb 16 How to commit changes to a docker image

Feb 5 How to make a triangle correlation heatmap with p-values labeled

Jan 29 10 tips for learning git

Jan 23 How to do gene correlation for single-cell RNAseq data (part 2) using meta-cell

Jan 13 How to do gene correlation for single-cell RNAseq data (part 1)

Jan 4 transpose single-cell cell x gene dataframe to gene x cell

2022 29 posts

Dec 30 Review 2022

Dec 18 How to run dockerized Rstudio server on google cloud

Dec 13 15 tools/papers for multi-sample multi-group single-cell RNAseq differential expression analysis

Dec 11 32 resources for (to-be) faculty on salary negotiation, grant writing, funding, and lab management

Dec 7 23 tools to work with (single-cell) TCR/BCR-seq immune repertoire data

Nov 29 7 links to deeply understand heatmap

Nov 28 6 training resources for data management

Nov 27 8 R/command line tools to deal with excel, tsv and csv files

Nov 15 8 Resources to study Transcription factor binding, enhancers and histone modification distribution

Nov 13 7 Books for you to learn bioinformatics

Nov 10 7 FREE Books to learn data science

Nov 9 12 resources to bookmark for reproducible computational research

Nov 7 9 tools for interactive exploring single-cell RNAseq data

Nov 7 8 links to BETTER understand principal component analysis (PCA)

Nov 3 5 tools to visualize genomic datasets

Nov 2 8 links to bookmark for better data visualization

Nov 1 6 links on workflow to make your life easier

Oct 28 16 resources for re-analyzing public expression data.

Oct 25 10 courses to get you started with bioinformatics

Oct 23 5 websites to analyze GEO RNAseq data without a single line of code

Oct 20 12 websites to learn computation and many others!

Oct 19 12 web tools to explore genomics data

Oct 17 10 tools to make a better flowchart than in PPT

Oct 14 10 websites for drawing scientific figures

Oct 6 Are PDL1 RNA and protein levels correlated in cancer cell lines?

Jul 3 use random forest and boost trees to find marker genes in scRNAseq data

Jun 16 Partial least square regression for marker gene identification in scRNAseq data

Jun 8 My odyssey of obtaining scRNAseq metadata

May 15 marker gene selection using logistic regression and regularization for scRNAseq

2021 7 posts

Dec 31 Review 2021

Dec 1 Obtain metadata for public datasets in GEO

Oct 17 Be careful when left_join tables with duplicated rows

Aug 26 Matrix Factorization for single-cell RNAseq data

Aug 7 How to test if two distributions are different

Mar 10 clustered dotplot for single-cell RNAseq

Jan 25 Precious lessons I learned from my Mom

2020 13 posts

Dec 31 Review 2020

Oct 2 compare slopes in linear regression

Sep 10 Enhancement of scRNAseq heatmap using complexheatmap

Aug 26 dplyr::count misses factor levels: a case in comparing scRNAseq cell type abundance

Jul 15 setting up Travis CI for github repos

Jul 2 build your own singularity image

May 23 customize FeaturePlot in Seurat for multi-condition comparisons using patchwork

Mar 17 stacked violin plot for visualizing single-cell data in Seurat

Mar 5 Monty Hall problem- a peek through simulation

Feb 21 compare kallisto-bustools and cellranger for single nuclei sequencing data

Feb 18 cellranger mk reference with transgenes

Feb 7 Align multiple ggplot2 plots by axis

Feb 4 add pct_in for each cluster for scRNAseq result table using list column

2019 17 posts

Dec 29 The end of 2019

Dec 11 Mixing mouse and human 10x single cell RNAseq data

Nov 26 Modeling single cell RNAseq data with multinomial distribution

Nov 21 negative bionomial distribution in (single-cell) RNAseq

Nov 13 negative binomial distribution

Sep 12 My opinionated selection of books/urls for bioinformatics/data science curriculum

Aug 6 Develop Bioconductor packages with docker container

Jun 9 Run Rstudio server with singularity on HPC

May 29 Calculate scATACseq TSS enrichment score

May 3 clustering scATACseq data: the TF-IDF way

Apr 29 plot 10x scATAC coverage by cluster/group

Feb 22 Use docopt to write command line R utilities

Feb 14 Split a 10xscATAC bam file by cluster

Feb 6 understand 10x scRNAseq and scATAC fastqs

Jan 28 How to make a transcript to gene mapping file

Jan 13 Understanding p value, multiple comparisons, FDR and q value

Jan 4 permutation test for PCA components

2018 18 posts

Dec 28 The end of 2018

Dec 19 A tale of two heatmap functions

Dec 18 PCA in action

Nov 27 Three gotchas when using R for Genomic data analysis

Nov 27 Merge featureCount table from RNAseq

Oct 10 open files on remote with sublime by ssh

Oct 9 set up odyssey HPC dot files

Oct 4 set up ssh odyssey HPC

Oct 3 set up my new mac laptop

Sep 7 Compute averages/sums on GRanges or equal length bins

Jun 30 my first try on Rmarkdown using blogdown

Jun 29 hugo academic theme blog down deployment (some details)

Jun 27 Backup automatically with cron

Jun 22 How to upload files to GEO

May 16 get the peaks that shared in multiple samples

Feb 6 convert a human gmt file to mouse for GSEA

Jan 24 ATACseq contamination of mycoplasma DNA

Jan 2 cancer gene census copy number

2017 19 posts

Dec 31 The End of 2017

Dec 20 Merge Enhancer promoter interaction bedpe files and recursive function in R

Nov 22 run gistic2 with sequenza segmentation output from whole exome sequencing

Sep 27 Use annovar to annotate variants

Aug 10 bwa-mem multi-mapping reads

Aug 4 dangerous rm command

Jul 13 mount smb on ubuntu

Jul 10 cores, cpus and threads

Jun 28 install VEP for annotating variants

Jun 15 bwa aln or bwa mem for short reads (36bp)

Jun 5 Weather and crimes in Chicago

May 22 when NAs are not NAs

Apr 20 SHERLOCK to detect early circulating tumor DNA

Apr 20 several very interesting histone modification (epigenetics) papers

Apr 19 sshfs on ubuntu and ssh key

Feb 24 use bash associate array to generate commands

Feb 1 How to enable the scroll mode for tmux

Jan 30 How to make a heatmap using character matrix

Jan 3 reorder boxplot according to median

2016 23 posts

Dec 27 The End of 2016

Nov 25 compare boxplot, violin plot and sina plot

Nov 14 define intronic, exonic and intergenic regions using GRanges

Oct 20 why not stringsAsFactors: my personal experience

Oct 2 Cutting out 500 columns from a 26G file using command line

Sep 12 Heatmap demystified part II: Using heatmap to represent continuous values

Aug 17 Heatmap demystified part I: use heatmap to represent discrete values

Aug 13 bring the power of R to command line

Aug 1 Gene Set Enrichment Analysis (GSEA) explained

Jul 19 several databases I want to share for RNA-seq data

Jul 11 Comparing salmon, kalliso and STAR-HTseq RNA-seq quantification

Jul 4 Misconcept of Epigenetics

Jun 30 How to deal with paired samples for snakemake

May 29 My first ever minimal working ChIP-seq pipeline using snakemake

May 5 Downsampling bam files to a certain number of reads

Apr 25 extract all kinds of archives on the fly using extract command

Apr 20 library size normalization for ChIP-seq

Mar 25 The most powerful unix commands I have learned so far: find + parallel

Mar 3 Breakpoints clustering for structural variants

Feb 24 install shellcheck in atom

Feb 7 read in all the files in a folder to R

Jan 25 Upset plot for overlapping ChIP-seq peaks: an alternative to Venn diagram

Jan 7 find the nearest upstream genes using GRanges

2015 27 posts

Dec 23 Using wget to download specific files from ftp but avoiding the directory structure

Nov 5 How to make a box-plot with jittered points for multiple groups

Nov 2 convert html to pdf by pandoc

Oct 29 merge the sub-cytobands to major cytoband and get the coordinates

Oct 22 Cytogenetic band explained

Oct 6 convert bam to fastq and remap it with bwa mem

Sep 14 MACS2 parallel peak calling

Sep 3 mount a remote server on mac using SSHFS

Aug 25 sort with header maintained

Aug 13 2 cents on coding from a bioinformatics beginner

Aug 4 linux command join with header

Jul 21 I promised a post with heatmaps, and I delivered more with PCA, MDS and clustering

Jul 14 Materials for the 1st Summer Institute in Statistics for Big Data

Jul 2 String manipulation in bash

Jun 23 RPKM/FPKM, TPM and raw counts for RNA-seq

Jun 23 ChIP-seq analysis part1

May 20 change the mac terminal color scheme and use oh my zsh!

May 19 Using Awk to format the gene expression file to gct format for Gene Set Enrichment Analysis (GSEA)

May 14 Using Awk to join two files based on several columns

May 4 IBash Notebook for reproducible research

Apr 30 get all the promoter sequences of human hg19 genome

Apr 23 simulation of distribution of means draw from exponential distribution

Apr 6 My first Software Carpentry workshop as an instructor

Mar 22 benchmarking for shuf vs fast_sample

Feb 24 fetch genomic sequences from coordinates

Jan 26 use Entrez Direct to access NCBI database

Jan 23 Install Inkscape on Mac

2014 31 posts

Nov 10 csvkit to manipulate csv at command line, Rio to interact with R at command line

Oct 30 Test significance of overlapping genes from 2 gene sets

Oct 23 convert bam file to bigwig file and visualize in UCSC genome browser in a Box (GBiB)

Oct 22 speed up grep

Sep 26 everyone will write a blog post on dplyr

Sep 11 make a soft link

Sep 10 converting gene ids using bioconductor with biomaRt and annotation packages

Sep 3 mapping gene ids with mygene

Aug 14 rename a bunch of files with bash by regular expression

Aug 8 R commands basics

Aug 7 Understanding the Forward strand and Reverse strand and the coordinates systems

Aug 6 linux commands basics

Jul 25 run a local blast

Jul 22 use python to change the header of a fasta file based on a dictionary in another file

Jul 4 get an idea of a gene expression value across samples by GEOquery

Jun 26 quality control of your fastq file! my first post after I got my PhD!

Jun 17 & or && operator in R

May 27 MACS for Dnase-seq data

Apr 14 order a matrix by a pre-defined group and then by the rowSums in R

Apr 11 rehead a bam file

Apr 4 liftover wig file

Mar 18 qseq to fastq conversion

Mar 12 Several NGS bioinformatics training materials

Mar 3 Unix sort except the first line

Feb 24 interactive visualization packages for R and python

Feb 18 hosting bigwig by dropbox for UCSC visualization

Feb 13 how to get a genome-wide motif bed file

Feb 6 several tools for Hi-C data, ChIP-seq and methylation data

Jan 28 manipulate GTF file with AWK

Jan 23 MeDIP-seq and histone modification ChIP-seq analysis

Jan 20 ChIP-seq analysis programs

2013 108 posts

Dec 19 log2 fold gene expression change heatmap

Dec 17 ChIP-seq peaks overlapping significance test

Dec 11 Tet1 enrichment at CpG rich-promoters

Dec 7 GEOquery to access GEO datasets

Dec 3 explain shell

Nov 21 mysql to get all the disease associated SNPs

Nov 19 mysql rocks

Nov 16 ChIP-exo data analysis

Nov 11 So you want to be a computational biologist?

Nov 1 DESeq work flow

Oct 31 python code for getting the reverse complement DNA strand

Oct 30 My first play with GRO-seq data, from sam to bedgraph for visualization

Oct 24 useful unix one liners for bioinformatics

Oct 18 group the same ID to the same line by python, use awk to do SQL like groupby and sum

Oct 11 A beginner’s guide to bioinformatics Fwd Homologus

Oct 8 Does every new biology PhD student need to learn how to program?

Oct 7 choose random lines from a file

Oct 3 compare ChIP-seq data for different conditions and different transcription factors?

Oct 1 RNA-seq analysis samtools sort and htseq-count

Sep 26 Three ways to change a space delimited file to a tab delimited file

Sep 24 finding the closest feature given a set of Genomic coordinates

Sep 20 Genomic Interval Tree, Interval manipulation

Sep 17 Amazing GNU sort

Sep 17 Tophat run time

Sep 17 Detect mutations from RNA-seq data

Sep 13 The Backtick in the linux command

Sep 12 FPKMs and counts compared for RNA-seq data

Sep 11 reproduce k-means clustering and heatmap

Sep 5 RNA-seq step by step demonstration

Aug 29 A new peak calling software: peakzilla

Aug 29 web/GUI tools for biological data analysis

Aug 27 Two nature protocols for RNA-seq analysis

Aug 27 How to make a heatmap based on ChIP-seq data by R

Aug 21 install GIMP 2.8 in Ubuntu 12.04

Aug 15 pdf organizer and reference manager

Aug 14 Decorators in python

Aug 12 Two pipelines for NGS analysis

Aug 9 Very good R tutorial by Google developer

Aug 8 nice demonstration of *args and **kwargs in python function def

Aug 8 python for biologist

Aug 1 UCSC genome browser tutorial

Jul 31 tools for circular representation of omics data

Jul 25 DESeq2 is now in Bioconductor

Jul 23 jMOSAiCS: joint analysis of multiple ChIP-seq datasets

Jul 20 install bioawk in unbuntu

Jul 20 ubuntu 12.04 networking restart

Jul 17 Computational Competence for Biologists

Jul 16 run ipython in emacs, matplotlib after plot.show( ), the ipython buffer remains hanging

Jul 12 yes, you need to validate the genomic discoveries

Jul 4 a python script for extracting fastq sequences

Jul 1 book recommendation: Sed & Awk 101 Hacks

Jul 1 The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability

Jun 29 VCF file annotation and manipulation tools

Jun 26 bubble sort and merge sort

Jun 25 use sed to print out every n lines, split pair-end FASTQ file

Jun 18 count how many mapped reads in a bam file

Jun 17 sashimi_plot for RNA-seq data

Jun 12 define a python function--- find the biggest number of a list

Jun 11 FASTA/Q file manipulation tool readfq

Jun 8 My personal suggestions to get started with bioinformatics

Jun 7 encouraging ! How I Taught Myself to Code in Eight Weeks

Jun 7 remap the Eland sorted.txt file from hg18 to hg19

Jun 6 My first try on Git

Jun 1 Using R and Bioconductor for proteomics data analysis

Jun 1 count ChIP-seq, RNA-seq counts at features

Jun 1 A very good introduction of NGS analysis in the HOMER page

Jun 1 convert Eland sorted.txt to bam file

May 30 Genome browsers

May 29 Run APE plasmid editor in linux

May 23 Scaling variant detection pipelines for whole genome sequencing analysis from Blue collar bioinformatics

May 21 Voom! Precision weights unlock linear model analysis tools for RNA-Seq read counts

May 20 what are phased and unphased genotypes?

May 17 Use tabix to extract subset of SAM, bed and VCF files

May 17 Find exons introns and intergenic regions

May 17 RNA-seq assembler STAR

May 16 linux command join

May 16 Awk Command to Count Total, Unique, and the Most Abundant Read in a FASTQ file

May 16 How to stay the current of bioinformatics

May 13 Framework for evaluating variant detection methods: comparison of aligners and callers

May 13 RNA-seq analysis tools

May 11 batch convert youtube video to mp3

May 8 0-based and 1-based coordinates

May 7 SRA file and my first Bowtie run on UF HPC (high performance computing center)

May 2 download all the stuff from a website by wget

Apr 30 make an average conservation plot based on ChIP-seq data

Apr 30 batch converting coordinates to sequences

Apr 23 slow google chromium in ubuntu solved

Apr 22 awk for simple text manipulation

Apr 20 Liftover between different Genome assemblies (hg18 to hg19)

Apr 16 Statistical measure of biological significance for overlapping genomic regions

Apr 8 custom sort in python, the built-in sorted()

Apr 6 python scripts for real bioinformatic problems

Apr 6 How to make TSS plot using RNA-seq and ChIP-seq data

Apr 4 Must read blog

Apr 4 Cool use of Unix paste with NGS sequences:FASTQ to FASTA

Apr 4 The Zen of Python

Apr 4 What does __name__ == "__main__" mean?

Apr 4 use linux commands to extract lines from a file by line number

Apr 3 python packages for bioinformatics

Apr 3 Sorting genomic alignments using Python

Apr 3 Trimming adaptors from short read sequences

Apr 3 python and Bioconductor for differential gene expression and gene ontology analysis

Apr 3 Bioinformatics resources

Apr 2 Genomic Interval manipulation

Apr 1 long integers and float numbers in python

Mar 30 check file and folder size in linux

Mar 30 recursion in python

Mar 30 download data from UCSC database to local drive