Single-base-resolution detection of RNA epitranscriptomic modifications — from method to pipeline.

m5C-UBSseq
Ultrafast bisulfite sequencing for m⁵C detection

pseudoU-BIDseq
Detecting Ψ (pseudouridine) modification at single-base resolution

m6A-SACseq
Optimized protocol & pipeline for m⁶A-SAC-seq

m6A-CAMseq
Pipeline for m⁶A-CAM-seq

m6A-eTAMseq
Enzymatic method for assaying m⁶A at single-base resolution

pseudoU-PUMseq
Ψ-PUMseq pipeline for pseudouridine detection

dichromat
Containerized conversion sequencing (eTAM-seq, CAM-seq, GLORI, BS-seq): mapping → site-calling → reporting

General pipelines for bioinformatics analysis (not RNA-modification detection).

SLOTH
Single-cell lineage tracing on Targeted Hypermutation

smallRNA-prism
Small RNA sequencing analysis pipeline — 🔒 WIP

scmd-calmorph
Quantify morphological traits of budding yeast

Bioinformatics tooling: alignment, QC, visualization & reporting.

countmut
Unified ultra-fast strand-aware mutation counter — C core + Python wrapper; fuses pileup & read-walk counting, mate-overlap dedup, samtools-style -e/-p filters, base-count & allele/VCF output

coralsnake
Exon-aware RNA analysis pipeline — splice-aware BAM liftover, site/variant annotation, metagene & motif analysis (successor to metagene & variant)

sanger
Sanger sequencing toolkit — chromatogram visualization, mutation calling, QC, base-calling, trimming, assembly & export (CLI + Python + MCP)

cutseq
Trim sequencing adapters from NGS data automatically

igvplot
IGV-style BAM read pileup / coverage / gene-feature / sashimi plots in matplotlib (pysam + dna_features_viewer), with per-base mismatch & epigenetic-modification detail

webblast
NCBI BLAST client CLI — submit, poll & cache web BLAST searches with colored output

Utilities & experiments

llmtop
Real-time terminal dashboard for LLM inference servers (GPU, throughput, speculative decoding)

hey
Some useful / useless commands

graph-easy-py
Python port of Graph::Easy — render graphs as ASCII art