Research pipeline
Integrated plant small RNA-seq analysis
TRMRNAseqTools
Problem
Plant small RNA studies often depend on fragmented preprocessing, annotation, and counting steps that are difficult to reproduce across datasets.
My contribution
I built a Shell and Python workflow that automates read processing, hierarchical RNA annotation, length profiling, and miRNA re-annotation.
Value
A reusable analysis path from raw small RNA-seq reads to interpretable plant RNA summaries.
Plant small RNAPipelinePython
View repositoryMethod development
Parallel profiling of miRNA 3-prime modifications
Tailing / trimming workflow
Problem
Non-templated tailing and trimming events are biologically informative but difficult to recover and compare across many small RNA-seq samples.
My contribution
I consolidated the analysis into a parallel workflow that reconstructs modification profiles, supports UMI libraries, and integrates genome and feature-level summaries.
Value
Restartable multi-sample analysis with per-miRNA profiles, tail-base statistics, and publication-ready visual outputs.
miRNARNA modificationReproducibility
View repositoryPublished research
Reproducible analysis for RNA modification discovery
PBOX-sRNA-seq
Problem
Specialized small RNA libraries need analysis code that connects sequencing evidence to specific terminal RNA modifications.
My contribution
I contributed the analysis code used to generate results for the PBOX-sRNA-seq study published in Nucleic Acids Research in 2024.
Value
A transparent computational record supporting discoveries in miRNA modification and modified 5-prime tRNA fragments.
PublicationsRNA-seqRNA modification
View repositoryResearch engineering
From raw reads to differential and splicing analysis
Bulk RNA-seq workflow
Problem
Bulk RNA-seq projects become fragile when quality control, mapping, counting, differential expression, and reporting are run as disconnected scripts.
My contribution
I designed a modular 13-step workflow covering validation, QC, rRNA filtering, mapping, gene and miRNA counting, DE analysis, alternative splicing, and reporting.
Value
A restartable and auditable workflow that keeps analysis definitions, contrasts, and outputs aligned across a study.
RNA-seqDESeq2Workflow
View repositoryResearch engineering
One-command methylome processing and reporting
WGBS analysis
Problem
WGBS analysis combines expensive alignment, context-aware methylation calls, cohort QC, and many downstream figures that must remain restartable.
My contribution
I built a validated entry point for QC, Bismark mapping, methylation extraction, metaprofiles, summaries, and publication figures.
Value
A reproducible methylome workflow with configuration checks that prevent incompatible results from being silently reused.
EpigenomicsWGBSAutomation
View repositoryVisualization tool
Inspect small RNA evidence in genomic context
sRNA Track Viewer
Problem
Small RNA loci are easier to evaluate when read distributions and annotations can be inspected together instead of compared across static files.
My contribution
I developed a focused viewer for exploring small RNA sequencing tracks and locus-level evidence.
Value
A more direct way to review patterns, compare regions, and communicate sequencing evidence.
VisualizationSmall RNAGenomics
View repository