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deepcelllineage

3 indexed repositories · View on GitHub

dpmitolin
Use mitochondrial sequence from single cells to determine cell lineage relationships with deep learning

4 stars
mitolin
Use mitochondrial sequence from single cells to determine cell lineage relationships

Jupyter Notebook · 2 stars
fluHA
For pipeline development starting with flu HA fasta files

Jupyter Notebook · 1 star

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20 open issues indexed

Modify embedding visualiser to display embeddings of genomic data Open

deepcelllineage/dpmitolin#2 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Modify single cell data pre-processing pipeline to align to human genome Open

deepcelllineage/dpmitolin#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Create python wrapper for a kmer counting utility implemented in C++ Open

deepcelllineage/dpmitolin#4 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
boilerplate notebooks and utility scripts for moving data files to/from cloud storage Open

deepcelllineage/dpmitolin#5 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Generate 3D images of flu HA proteins with variants highlighted Open

deepcelllineage/fluHA#2 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Generate graphs of flu ILI and subtype prevalence Open

good first issue

deepcelllineage/fluHA#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Create an Alignment of H3N2 Strains With Minimal Gaps Open

deepcelllineage/fluHA#4 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Extract chromosome M data Open

1-4 hours basic bash or python easy (relatively) good first issue

deepcelllineage/mitolin#5 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Create a "Panel of Normals" Open

>12 hours mentally challenging quirks of the field

deepcelllineage/mitolin#6 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Align and visualize multiple (mitochondria) nucleotide sequence (.fasta) files Open

4-12 hours good first issue quirks of the field

deepcelllineage/mitolin#7 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Annotate mitochondrial DNA fasta files with genes Open

>12 hours good first issue quirks of the field

deepcelllineage/mitolin#8 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Create an architecture for open source data exchange Open

4-12 hours good first issue

deepcelllineage/mitolin#9 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Generate a text file with cytochrome b function and pathway attributes Open

4-12 hours good first issue quirks of the field

deepcelllineage/mitolin#10 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Annotate a-helices, b-sheets, and loops of mitochondiral protein cytochrome b Open

>12 hours good first issue quirks of the field

deepcelllineage/mitolin#11 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Write a tutorial that explains how nucleotide distance matrices are generated Open

4-12 hours basic bash or python good first issue quirks of the field

deepcelllineage/mitolin#12 · 3 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Label cells with B, LP, & LT classes Open

1-4 hours easy (relatively) good first issue

deepcelllineage/mitolin#15 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Find Distance Calculation in source code from Chang Lab Open

help wanted

deepcelllineage/mitolin#16 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Find Distance Calculation in source code from Sankaran Lab Open

help wanted

deepcelllineage/mitolin#17 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Update fastq2vcf script according to mitolin plan Open

enhancement

deepcelllineage/mitolin#19 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Use gatk's farm to convert vcf2fasta Open

new feature

deepcelllineage/mitolin#20 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026

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