This repository contains some scripts I wrote for analyses and efficiency.

List of scripts

Trio-binning genome assembly, recombination landscape

• 20240722extract_seq_append_to_fasta.py
• 20240722rm_seq_from_fasta.py

Full report: https://docs.google.com/document/d/1vZzuElzgIKpSqNFux41Lmt7raKhQ-RQqhkXuGneilHM/edit?usp=sharing.

Nucleosome-removed single-cell ATAC-seq data analysis

• 20231008scATAC_recomb_qc.md (all scripts merged into this .md)

Full report: https://docs.google.com/document/d/1Cm1XDc0TmMHJJIGBLbFP2rR463NN_ZfrIEGrjmzgFBc/edit?usp=sharing.

Single-cell same-cell RNA/ATAC-seq integration ("integrateRNA_ATAC")

• 20230206seurat.R
• 20230206signac.R
• 20230208archR.R
• 20230224doublet.R
• 20230316portal.ipynb (see: YangLabHKUST/Portal#6)
• 20230223scrublet.ipynb

Single-cell RNA-seq ("scRNAseq")

• 20220315qc.R (quality control visualizations)
• 20220325merge.R (merge datasets sequenced from multiple samples)
• 20220407normalize.R
• 20220413clustering.R
• 20220425trajectory.R
• 20220518trajectory_function.R (clean code organized into functions)
• 20220512dispersion_on_server.R
• 20220614loom_viz.R
• 20220701loom_heatmap.R

Bulk RNA-seq ("bulkRNAseq")

• 20220625DESeq2.R
• 20220628GO.KEGG.R
• 20220720loom_viz_func.R

Tools (details see bottom)

• GetGeneID.py
• GetMGIMarker.py

Misc ("misc")

• 20220315ms.R: mass spectrometry data clustering
• 2018-2019: plant duplicate gene retention scripts: https://drive.google.com/drive/folders/1vftU-BLgMZeUw42-xUxTfKDPOa_Gy6qy?usp=sharing

Tools

GetGeneID.py

Last update: 2022 May 09. Required package: selenium. Required installation: chromedriver. Written with Python 3.10.0.

Purpose: Bulk convert human marker IDs to Rhesus monkey gene ID and Ensembl ID from NCBI Gene (https://www.ncbi.nlm.nih.gov/gene).

Usage:

• Enter the path where you installed the chromedriver.
• Replace the human marker IDs in the input list l.
• Replace the 'rhesus' if you are searching for another organism (organism must be present in the NCBI Gene database).
• Run the script.
• Results will be printed to the console.

GetMGIMarker.py

Last update: 2020 Dec 13 (Script may be outdated due to selenium update, see GetGeneID for updated usage). Required package: selenium. Written with Python 3.8.3.

Purpose: Bulk convert protein names to marker IDs for Seurat input. Scrapes info from: http://www.informatics.jax.org/batch/summary.

Usage:

• Use text editor to replace the list of mRNA/protein names with your search terms and run the script.
• Results will be returned to the console.