The archr-h5ad from mvinyard

archr-h5ad's Introduction

I'm currently working on my PhD at Harvard University where I am developing methods for the analysis of single-cell genomics data. I also work on methods for CRISPR-Cas9-based genome-editing tools (like base-editing) to study cancer progression. My PhD work is funded by an NIH F31 award through the NCI and focuses on applying innovations in deep learning to analogous problems in the analysis of single-cell data. You can read more about me and my studies at my website.

I am passionate about and interested in:

🧿 (single-cell) epigenomics and chromatin biology
🧬 Functional annotation of variation in the human genome
🧮 Deep learning
✂️ Functional CRISPR studies
🧠 Psychiatric disorders
🧫 Cancer biology
🐍 Implementing open-source tools for genomics in python.
🎨 Computer graphics art

Repos and software libraries

Deep learning

Bioinformatics: CRISPR and other assays (single-cell and bulk)

Python developer utility packages and plotting

For tutorials and resources: link

GitHub Stats

Selected Publications and preprints

CRISPR-suppressor scanning reveals a nonenzymatic role of LSD1 in AML

Michael E. Vinyard, et al. . Nat. Chem. Biol. DOI: 10.1038/s41589-019-0263-0 (2019).

Assessement of computational methods for the analysis of single-cell ATAC-seq data

Chen, H., Lareau, C.†, Andreani, T.†, Michal E. Vinyard†, et al. . Genome Biol. DOI: 10.1186/s13059-019-1854-5 (2020).
GitHub

SIMBA: SIngle-cell eMBedding Along with features

Huidong Chen, Jayoung Ryu, Michael E. Vinyard, Adam Lerer, & Luca Pinello. . bioRxiv, DOI: 2021.2010.2017.464750 (2021).
GitHub
docs

Current progress and potential opportunities to infer single-cell developmental trajectory and cell fate

L. Wang†, Q. Zhang†, Q. Qin†, N. Trasanidis†, Michael E. Vinyard†, et al., . Curr. Opin. in Syst. Biol. ISSN 2452-3100. DOI: 10.1016/j.coisb.2021.03.006 (2021).

singlecellVR: interactive visualization of single-cell data in virtual reality

Stein, D.†, Chen, H.†, Vinyard, M.E.†, et al. . Front. genet. DOI: 10.1101/2020.07.30.229534 (2021).
GitHub
singlecellVR.com

Dyanmically generated stats are implemented from GitHub Readme Stats

† denotes equal contribution

archr-h5ad's People

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archr-h5ad's Issues

error reading arrow file

Hello,

An error was encountered when I read the arrow file with the following input:

adata = ArchR_h5ad.read_arrow('S5.arrow', use_matrix="TileMatrix")

Was it due to a lot of variables with 0 counts in the TileMatrix? Thank you.

Reading ArchR TileMatrix to AnnData
Chromosomes: 0%| | 0/23 [00:00<?, ?it/s]

Traceback (most recent call last):
File "", line 1, in
File "/home/pc/miniconda3/envs/snap/lib/python3.10/site-packages/ArchR_h5ad/_main/_read_arrow_to_adata.py", line 66, in _read_arrow_to_adata
arrow.to_adata(use_matrix=use_matrix, write_h5ad=write_h5ad)
File "/home/pc/miniconda3/envs/snap/lib/python3.10/site-packages/ArchR_h5ad/_main/_Arrow.py", line 52, in to_adata
self._adata = _compose_anndata(DataDict=self._DataDict,
File "/home/pc/miniconda3/envs/snap/lib/python3.10/site-packages/ArchR_h5ad/_compose_adata/_compose_anndata.py", line 27, in _compose_anndata
adata = _add_obs_var(adata, metadata, feature_df)
File "/home/pc/miniconda3/envs/snap/lib/python3.10/site-packages/ArchR_h5ad/_compose_adata/_add_obs_var.py", line 49, in _add_obs_var
adata.var = _add_var(feature_df)
File "/home/pc/miniconda3/envs/snap/lib/python3.10/site-packages/anndata/_core/anndata.py", line 882, in var
self._set_dim_df(value, "var")
File "/home/pc/miniconda3/envs/snap/lib/python3.10/site-packages/anndata/_core/anndata.py", line 798, in _set_dim_df
value_idx = self._prep_dim_index(value.index, attr)
File "/home/pc/miniconda3/envs/snap/lib/python3.10/site-packages/anndata/_core/anndata.py", line 810, in _prep_dim_index
raise ValueError(
ValueError: Length of passed value for var_names is 11627605, but this AnnData has shape: (1590, 6062095)

read_arrow() fails when metadata contains Nonetype

Sometimes, a null value may be added to the arrow file metadata dict. I need to add a flag to specifically note this and move on. Currently, it breaks the function.

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