Bioinformatics Γγ°γ€ RNA epigenetics β open-source pipelines for
single-base-resolution RNA modification detection (m5C Β· m6A Β· Ξ¨) and NGS tooling.
Single-base-resolution detection of RNA epitranscriptomic modifications β from method to pipeline.
m5C-UBSseq stars since 2023
Ultrafast bisulfite sequencing for m5C detection
pseudoU-BIDseq stars since 2022
Detecting Ξ¨ (pseudouridine) modification at single-base resolution
m6A-SACseq stars since 2022
Optimized protocol & pipeline for m6A-SAC-seq
m6A-CAMseq stars
Pipeline for m6A-CAM-seq
m6A-eTAMseq stars
Enzymatic method for assaying m6A at single-base resolution
pseudoU-PUMseq stars
Ξ¨-PUMseq pipeline for pseudouridine detection
dichromat stars new
Containerized conversion sequencing (eTAM-seq, CAM-seq, GLORI, BS-seq): mapping β site-calling β reporting
General pipelines for bioinformatics analysis (not RNA-modification detection).
SLOTH stars since 2018
Single-cell lineage tracing on Targeted Hypermutation
smallRNA-prism π WIP (not public yet)
Small RNA sequencing analysis pipeline β π WIP
scmd-calmorph stars since 2016
Quantify morphological traits of budding yeast
Bioinformatics tooling: alignment, QC, visualization & reporting.
countmut stars active
Unified ultra-fast strand-aware mutation counter β C core + Python wrapper; fuses pileup & read-walk counting, mate-overlap dedup, samtools-style -e/-p filters, base-count & allele/VCF output
coralsnake stars
Exon-aware RNA analysis pipeline β splice-aware BAM liftover, site/variant annotation, metagene & motif analysis (successor to metagene & variant)
sanger stars since 2018
Sanger sequencing toolkit β chromatogram visualization, mutation calling, QC, base-calling, trimming, assembly & export (CLI + Python + MCP)
cutseq stars
Trim sequencing adapters from NGS data automatically
igvplot stars new
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 β submit, poll & cache web BLAST searches with colored output
Utilities & experiments
llmtop new
Real-time terminal dashboard for LLM inference servers (GPU, throughput, speculative decoding)
hey stars since 2018
Some useful / useless commands
graph-easy-py new
Python port of Graph::Easy β render graphs as ASCII art
ποΈ Superseded / archived tools β replaced by newer tools (see each badge)
metagene stars since 2022 superseded by coralsnake
Metagene profiling analysis & visualization β
variant stars since 2021 superseded by coralsnake
Python utilities for genomic variant analysis β
cpup stars since 2020 superseded by countmut
Convert samtools mpileup output to base-count tables (multi-BAM) β
mpileup stars since 2021 superseded by countmut
Rust base/indel pileup counter β
pbr stars since 2023 superseded by countmut
Pileup with Lua read/site filter expressions β
ποΈ Organizations