ALLCools

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updates: - [github.com/psf/black: 24.3.0 → 24.4.2](https://github.com/psf/black/compare/24.3.0...24.4.2)

pre-commit-ci[bot]

previous support for ballc adding a cmeta_path arg to function extract_allc which breaks the cli extract-allc function. fixed in this commit

jksr

Could provide some example file format?

3

Hello, Can you provide example file of meta data? And how to create the hg38_genecode_v28.geneslop2k.bed.gz, promoter_slop2k.sorted.bed.gz, hg38_CGI.sorted.bed.gz files? Does slop represent adding 2000bp before and after the region? Thank you.

ryuzheng

I followed the instructions in the documentation - using a .yaml file to make a mamba environment, but got the following error: Executing transaction: | Traceback (most recent call last):...

timblosser

Hi, I was using ALLCools on the Lee et al. 2019 single-cell methylation data (https://pubmed.ncbi.nlm.nih.gov/31501549/). The code I use to generate the mcds data is something like below: allcools generate-dataset...

sshen82

Hi Hanqing: Hope you're well! I was using `extract-allc` to merge CG counts across strands on version 1.0.8 of allcools. I encountered the following and wanted to check if this...

chooliu

Dear team, Thanks for developing this great tool! I noticed a minor issue when using the function `highly_variable_methylation_feature()` as defined in `ALLCools/mcds/utilities.py` `n_top_feature` is supposed to be a parameter that...

tdietl

updates: - [github.com/psf/black: 24.4.2 → 24.10.0](https://github.com/psf/black/compare/24.4.2...24.10.0) - [github.com/asottile/blacken-docs: 1.18.0 → 1.19.0](https://github.com/asottile/blacken-docs/compare/1.18.0...1.19.0) - [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.6.0...v5.0.0) - [github.com/PyCQA/flake8: 7.1.0 → 7.1.1](https://github.com/PyCQA/flake8/compare/7.1.0...7.1.1) - [github.com/asottile/pyupgrade: v3.16.0 → v3.17.0](https://github.com/asottile/pyupgrade/compare/v3.16.0...v3.17.0)

pre-commit-ci[bot]

I'm receiving an error during `mcds.get_score_adata` such that `quant_type='hyper-score' is not found` and `looking for quant_type='hyper_score'` I found in the mcds.py the following: `QUANT_TYPES` from: https://github.com/lhqing/ALLCools/blob/fb895c304b14960f8932c6e48cea10774f479676/ALLCools/mcds/mcds.py#L1025 are not aligning with...

agh-seq

Hi Hanqing, Thanks for the great package! When I use the integration module, I find it will report error when I plan to save it using `SeuratIntegration.save` with parameter `save_adata=True`....

beyondpie