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93 followers · 365 following

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Achievement: StarstruckAchievement: Pair ExtraordinaireAchievement: YOLOAchievement: Public SponsorAchievement: Arctic Code Vault ContributorAchievement: Pull Sharkx2

Achievements

Achievement: StarstruckAchievement: Pair ExtraordinaireAchievement: YOLOAchievement: Public SponsorAchievement: Arctic Code Vault ContributorAchievement: Pull Sharkx2

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y9c/README.md

👋 Hi, I'm Chang Ye

Bioinformatics × RNA epigenetics — open-source pipelines for single-base-resolution RNA modification detection (m⁵C · m⁶A · Ψ) and NGS tooling.

GitHub followers Blog


🏛️ Organizations

yclab
yclab yclab followers 		srils
srils srils followers

🧬 RNA modification pipelines

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

m5C-UBSseq stars
Ultrafast bisulfite sequencing for m⁵C detection

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

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

m6A-CAMseq stars
Pipeline for m⁶A-CAM-seq

trichromat stars new
General pipeline for 3-letter conversion sequencing methods

SLOTH stars
Single-cell lineage tracing on Targeted Hypermutation

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

pseudoU-PUMseq stars
Ψ-PUMseq pipeline for pseudouridine detection

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

🛠️ Analysis & NGS tools

Bioinformatics tooling: alignment, QC, visualization & reporting.

cfutils stars
Sanger chromatogram toolkit — trace visualization, mutation calling & QC

cutseq stars
Trim sequencing adapters from NGS data automatically

metagene stars
Metagene profiling analysis & visualization

cpup stars
Convert samtools mpileup output to base-count tables (multi-BAM)

Utilities & experiments

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

md2html
Generate styled HTML reports from Markdown files

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

Pinned Loading

  1. cfutils cfutils Public

    🧬 Chromatogram File Utils, a package that integrates trace visualization, mutation calling and quality control for Sanger sequencing data.

    Python 26 4

  2. cutseq cutseq Public

    ✂️ Trim sequencing adapters from NGS data automatically

    Python 14

  3. bwamem bwamem Public

    Python

  4. cpup cpup Public

    Convert mpileup format to base count tsv table

    C++ 4

  5. hey hey Public

    Some useful / useless commands

    Go 3

  6. biodart biodart Public

    🔬 A dart package for bioinformatics

    Dart 1