Nanopore-enabled Single-Cell Full-Length RNA-seq Analysis Pipeline for Comprehensive Transcriptomic Profiling

cuhk-haosun / course-MBI6013

Material for Msc. research project MBI6013

GNU General Public License v3.0

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Open Murui-da opened 3 months ago

Milokita commented 3 months ago

I would recommend using "Intergrated single-cell alternative splicing analysis using nanopore sequencing"

Murui-da commented 3 months ago

Cell Type	Database	DOI
renal cell carcinoma (RCC1, RCC2) melanoma (MEL1, MEL2) cancer cell lines A375 and H2030	GEO: GSE212945	https://doi.org/10.1038/s41467-023-39813-7
human lung adenocarcinoma cell lines (H2228, H1975, A549, H838 and HCC827) mixture	GEO: GSE154870
human induced pluripotent stem cell (iPSC)	ENA: PRJEB54718	https://doi.org/10.1186/s13059-023-02907-y
mouse muscle stem cells (MuSC)	GEO: GSE154868

Milokita commented 3 months ago

pls also specify does it offers FAST5 download

Murui-da commented 1 month ago

update the pipeline, adding a final report (only contains clustering and differential expression analysis for genes and isoforms).

Murui-da commented 4 weeks ago

Add IsoQuant software in the pipeline for novel isoforms discovery and comparison to known transcripts in reference.