Adjusted p-values: BH, BY, and FDR
Reading enrichment outputs and distinguishing adjustment methods from q-values.
Blog
Methods, analysis notes, and programming practice.
Undated
awk for identifiers and tabular data
Lookup tables, identifier replacement, duplicate FASTA headers, and field-specific operations.
Bash arrays
Declaring an array, expanding its elements, and checking its length.
Capturing standard error in a log
How shell redirection separates diagnostic messages from normal output.
Choosing a sort mode
Comparing lexical, numeric, general numeric, and version sorting.
Comparing CUT&RUN, CUT&Tag, and ChIP-seq
Learning notes on targeting, fragmentation, and protocol-specific tradeoffs.
GATK, DRAGEN, and long-read sequencing
Training notes on variant-calling error models and long-read capabilities.
grep patterns and matching options
Short examples of multiple patterns, case-insensitive matching, and text handling.
Investigating a Perl locale warning over SSH
A troubleshooting record for locale warnings observed on a remote server.
Looking up R objects by name
A short example of dynamic object lookup with get().
Notes on AUCell scoring
Exploring within-cell feature rankings and gene-set activity in single-cell analysis.
Python practice: a word game
Decomposed a word game into scoring, validation, hand management, and game control.
Python practice: bisection search
Compared linear search with bisection in an introductory programming assignment.
Python practice: functions and Hangman
Built helper functions, game loops, and a hint mechanism for a word game.
Python practice: recursion, classes, and inheritance
Worked through string permutations and class-based programming exercises.
R object systems: S3 and S4
Notes on classes, method dispatch, slots, and object-version compatibility.
Reading a GSEA plot
Contrasting a thresholded gene-list analysis with a ranked-list view.
Shell variables and parameter expansion
Notes on variable names, braces, and quoting paths.
Troubleshooting an unresponsive RStudio Server session
A case where excessive R Markdown output caused repeated browser-session failures.
Understanding Bowtie2 mapping quality
A research question about choosing a mapping-quality cutoff for samtools filtering.
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