scverse / scverse/scverse-io

IO functions: transcriptomics

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Description

Overview of IO functions related to transcriptomics to be included in the package.

Dependencies

pandas, numpy, scipy, h5py

excel: openpyxl
loom: loompy
zarr: zarr

Functions
  • read_h5ad
  • read_csv
  • read_excel
  • read_loom
  • read_mtx
  • read_umi_tools
  • read_zarr
  • read_10x_h5
  • read_10x_mtx
  • write_h5ad
  • write_zarr
  • write_csvs

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by locating the package entry points for the listed transcriptomics readers and writers, then review how the declared dependencies support each format. The work is complete when all named read and write functions are included with the corresponding format dependencies.

Written by the indexing model from the issue text.

Assessment

Tech stack
numpy, pandas
Domain
bioinformatics, data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

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