becavin-lab/checkatlas issues and pull requests

#48 - Implement metrics from Antoine Collin master thesis

Issue - State: open - Opened by drbecavin 8 months ago
Labels: enhancement

#47 - Add test datasets for spatial transcriptomics

Issue - State: open - Opened by drbecavin 8 months ago

#46 - Spatial Image QC

Issue - State: open - Opened by drbecavin 8 months ago

#45 - Tutorial for adding metrics in checklatlas

Issue - State: open - Opened by drbecavin 8 months ago
Labels: documentation, enhancement

#44 - Add test datasets

Issue - State: open - Opened by drbecavin 8 months ago
Labels: enhancement

#43 - Create github with all metrics

Issue - State: open - Opened by drbecavin 8 months ago
Labels: documentation

#42 - Add multiomic singlce cell mangamenet

Issue - State: open - Opened by drbecavin 8 months ago

#41 - Add SpatialData management

Issue - State: open - Opened by drbecavin 8 months ago
Labels: enhancement

#40 - Dimensionality reduction metrics

Issue - State: open - Opened by drbecavin 8 months ago
Labels: enhancement

#39 - Implement metrics from Malte Luecken's integration benchmark

Issue - State: open - Opened by drbecavin 8 months ago

#38 - Nf core

Pull Request - State: closed - Opened by drbecavin over 1 year ago

#37 - Multiqc

Pull Request - State: closed - Opened by drbecavin over 1 year ago

#36 - Improve Mito and ribo QC calculation

Issue - State: open - Opened by drbecavin over 1 year ago
Labels: enhancement, question

#35 - Integration to scVerse

Issue - State: open - Opened by drbecavin over 1 year ago
Labels: enhancement, question

#34 - Integration with nf-core pipelines

Issue - State: open - Opened by grst over 1 year ago - 5 comments
Labels: enhancement, question

#33 - Workflow

Pull Request - State: closed - Opened by drbecavin over 1 year ago

#32 - Metrics

Pull Request - State: closed - Opened by drbecavin almost 2 years ago - 1 comment

#31 - Metrics

Pull Request - State: closed - Opened by drbecavin almost 2 years ago

#30 - Metrics

Pull Request - State: closed - Opened by drbecavin almost 2 years ago

#29 - Metrics

Pull Request - State: closed - Opened by drbecavin almost 2 years ago - 1 comment

#28 - Switch to poetry

Pull Request - State: closed - Opened by drbecavin almost 2 years ago

#27 - Dim reduction metric management for seurat object

Issue - State: open - Opened by drbecavin over 2 years ago
Labels: bug, help wanted

#26 - Rpy2

Pull Request - State: closed - Opened by drbecavin over 2 years ago - 1 comment

#25 - Checkatlas conda, docker, singularity definition file

Issue - State: closed - Opened by drbecavin over 2 years ago - 2 comments
Labels: enhancement, question

#24 - Seurat import

Issue - State: open - Opened by drbecavin over 2 years ago - 1 comment
Labels: enhancement, question

#23 - Rpy2

Pull Request - State: closed - Opened by drbecavin over 2 years ago

#22 - Add Muon object

Issue - State: open - Opened by drbecavin over 2 years ago
Labels: enhancement, question

#21 - Add knee plots

Issue - State: closed - Opened by grst over 2 years ago - 5 comments
Labels: enhancement, question

#20 - Parse additional cellranger outputs

Issue - State: closed - Opened by chris-rands over 2 years ago - 3 comments
Labels: enhancement, help wanted, question

#19 - QC figures does not display parameters for Seurat object

Issue - State: closed - Opened by drbecavin over 2 years ago
Labels: bug, help wanted

#18 - Checkatlas .tsv tables in a separate folder

Issue - State: closed - Opened by drbecavin over 2 years ago - 1 comment
Labels: enhancement, question

#16 - Add management of information from integrated Atlas

Issue - State: closed - Opened by drbecavin over 2 years ago
Labels: enhancement, question

#15 - Write wiki/tutorial

Issue - State: closed - Opened by drbecavin over 2 years ago - 1 comment
Labels: documentation, enhancement

#14 - Problem of CPUs and ram utilization in multithread mode

Issue - State: closed - Opened by drbecavin over 2 years ago
Labels: bug, help wanted

#13 - Automatic/Semi-automatic search of celltype key

Issue - State: closed - Opened by drbecavin over 2 years ago
Labels: enhancement, help wanted, question

#12 - QC figures too big

Issue - State: closed - Opened by drbecavin over 2 years ago
Labels: enhancement, question

#11 - Fix parameters for checkatlas tools

Issue - State: closed - Opened by drbecavin over 2 years ago - 1 comment
Labels: enhancement, question

#10 - Umap with seurat_cluster does not display cluster

Issue - State: closed - Opened by drbecavin over 2 years ago - 1 comment
Labels: bug, help wanted

#9 - Add Kruskal stress calculation

Issue - State: closed - Opened by drbecavin over 2 years ago
Labels: enhancement, question

#8 - Multiome seurat object bad conversion

Issue - State: closed - Opened by drbecavin over 2 years ago
Labels: bug, enhancement, help wanted

#7 - Create summary html with multiqc

Issue - State: closed - Opened by drbecavin almost 3 years ago - 1 comment
Labels: enhancement, question