Ecosyste.ms: Issues

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GitHub / lmweber/osta issues and pull requests

#100 - hlc revision of crs-registration pr #79

Pull Request - State: closed - Opened by HelenaLC 23 days ago

#100 - hlc revision of crs-registration pr #79

Pull Request - State: closed - Opened by HelenaLC 23 days ago

#99 - img-segmentation

Issue - State: open - Opened by HelenaLC 24 days ago - 1 comment

#99 - img-segmentation

Issue - State: open - Opened by HelenaLC 24 days ago - 1 comment

#97 - minor revision of PR #96

Pull Request - State: closed - Opened by HelenaLC 24 days ago

#96 - Update img-qc chapter to use OSF

Pull Request - State: closed - Opened by drisso 24 days ago - 1 comment

#96 - Update img-qc chapter to use OSF

Pull Request - State: closed - Opened by drisso 24 days ago - 1 comment

#95 - book/packages title/acronym

Issue - State: open - Opened by HelenaLC 24 days ago - 9 comments
Labels: documentation

#95 - book/packages title/acronym

Issue - State: open - Opened by HelenaLC 24 days ago - 9 comments
Labels: documentation

#94 - contributing authors

Issue - State: open - Opened by HelenaLC 24 days ago - 3 comments
Labels: documentation

#94 - contributing authors

Issue - State: open - Opened by HelenaLC 24 days ago - 3 comments
Labels: documentation

#93 - img-workflow-cosmx

Issue - State: open - Opened by HelenaLC 24 days ago - 1 comment
Labels: workflow

#93 - img-workflow-cosmx

Issue - State: open - Opened by HelenaLC 24 days ago - 1 comment
Labels: workflow

#92 - img-quality-control (#81)

Pull Request - State: closed - Opened by HelenaLC 24 days ago

#92 - img-quality-control (#81)

Pull Request - State: closed - Opened by HelenaLC 24 days ago

#91 - colLabels() return NULL in seq-marker-genes

Issue - State: closed - Opened by Artur-man 24 days ago - 3 comments
Labels: bug

#91 - colLabels() return NULL in seq-marker-genes

Issue - State: closed - Opened by Artur-man 24 days ago - 3 comments
Labels: bug

#90 - +xen/vis workflow draft including data retrievely from OSF

Pull Request - State: closed - Opened by HelenaLC 25 days ago

#90 - +xen/vis workflow draft including data retrievely from OSF

Pull Request - State: closed - Opened by HelenaLC 25 days ago

#89 - reference fixes, updated DESCRIPTION, file cleaning

Pull Request - State: closed - Opened by HelenaLC 25 days ago

#89 - reference fixes, updated DESCRIPTION, file cleaning

Pull Request - State: closed - Opened by HelenaLC 25 days ago

#88 - crs-spat-stat

Pull Request - State: closed - Opened by HelenaLC 25 days ago

#88 - crs-spat-stat

Pull Request - State: closed - Opened by HelenaLC 25 days ago

#87 - datasets

Issue - State: open - Opened by HelenaLC 25 days ago - 4 comments
Labels: documentation

#87 - datasets

Issue - State: open - Opened by HelenaLC 25 days ago - 4 comments
Labels: documentation

#86 - Spat stat

Pull Request - State: closed - Opened by HelenaLC 25 days ago

#86 - Spat stat

Pull Request - State: closed - Opened by HelenaLC 25 days ago

#85 - seq-clustering

Pull Request - State: closed - Opened by HelenaLC 25 days ago

#85 - seq-clustering

Pull Request - State: closed - Opened by HelenaLC 25 days ago

#84 - bkg-infrastructure

Pull Request - State: closed - Opened by HelenaLC 26 days ago - 1 comment

#84 - bkg-infrastructure

Pull Request - State: closed - Opened by HelenaLC 26 days ago - 1 comment

#83 - bkg-infrastructure

Pull Request - State: closed - Opened by HelenaLC 26 days ago

#83 - bkg-infrastructure

Pull Request - State: closed - Opened by HelenaLC 26 days ago

#82 - Draft for seq-clustering-de

Pull Request - State: closed - Opened by peicai 26 days ago - 5 comments

#82 - Draft for seq-clustering-de

Pull Request - State: closed - Opened by peicai 26 days ago - 5 comments

#81 - Add img-QC chapter

Pull Request - State: closed - Opened by drisso 26 days ago

#81 - Add img-QC chapter

Pull Request - State: closed - Opened by drisso 26 days ago

#80 - Update img_clustering.qmd

Pull Request - State: open - Opened by Jieran-S 26 days ago - 4 comments

#80 - Update img_clustering.qmd

Pull Request - State: open - Opened by Jieran-S 26 days ago - 4 comments

#79 - crs-registration

Pull Request - State: closed - Opened by Artur-man 26 days ago - 3 comments

#79 - crs-registration

Pull Request - State: closed - Opened by Artur-man 26 days ago - 3 comments

#78 - seq - deconvolution

Issue - State: closed - Opened by HelenaLC 26 days ago - 1 comment

#78 - seq - deconvolution

Issue - State: closed - Opened by HelenaLC 26 days ago - 1 comment

#77 - bkg-infrastructure

Pull Request - State: closed - Opened by HelenaLC 26 days ago - 1 comment

#76 - bkg-infrastructure

Pull Request - State: closed - Opened by HelenaLC 26 days ago - 1 comment

#75 - aligned Xenium + Visium workflow

Issue - State: closed - Opened by HelenaLC 26 days ago - 1 comment
Labels: workflow

#74 - img-dimensionality-reduction and img-sub-cellular outlines

Pull Request - State: open - Opened by shazanfar 26 days ago - 1 comment

#73 - img - sub-cellular

Issue - State: open - Opened by shazanfar 26 days ago - 3 comments

#72 - first version of pp spatstat and intro to spat stat

Pull Request - State: closed - Opened by mjemons 27 days ago - 3 comments

#71 - Draft for crs-spat-stat and crs-spat-stat lattice

Pull Request - State: closed - Opened by sgunz 27 days ago - 2 comments

#70 - workflows

Issue - State: open - Opened by HelenaLC 27 days ago - 1 comment
Labels: workflow

#69 - draft for bkg-spatial-omics

Pull Request - State: closed - Opened by markrobinsonuzh 27 days ago - 4 comments

#68 - img - normalization

Issue - State: open - Opened by HelenaLC 27 days ago - 4 comments

#67 - Permission to redistribute publicly available datasets

Issue - State: closed - Opened by lmweber 28 days ago - 9 comments
Labels: question

#66 - img-clustering-de

Issue - State: open - Opened by Jieran-S 28 days ago

#65 - crs-spat-stat

Issue - State: closed - Opened by mjemons 28 days ago - 1 comment

#64 - crs - registration

Issue - State: closed - Opened by Artur-man 28 days ago

#63 - seq-deconvolution

Issue - State: open - Opened by estellad 28 days ago - 1 comment

#62 - seq - Visium HD workflow

Issue - State: open - Opened by lmweber 28 days ago - 2 comments
Labels: workflow

#61 - seq / img - Visium / Xenium workflows

Issue - State: closed - Opened by lmweber 28 days ago - 2 comments

#60 - bkg - spatial-omics

Issue - State: closed - Opened by lmweber 29 days ago - 5 comments

#59 - seq - clustering-de

Issue - State: closed - Opened by lmweber 29 days ago - 3 comments

#58 - seq - normalization, feature selection, dimensionality reduction

Issue - State: open - Opened by lmweber 29 days ago - 1 comment

#57 - seq - quality control

Issue - State: open - Opened by lmweber 29 days ago - 10 comments

#56 - crs - spatially variable

Issue - State: open - Opened by HelenaLC about 1 month ago - 5 comments

#55 - img - dimensionality reduction

Issue - State: open - Opened by HelenaLC about 1 month ago - 6 comments

#54 - crs - feature sets & signatures

Issue - State: open - Opened by HelenaLC about 2 months ago

#53 - img - cell-cell communication

Issue - State: open - Opened by HelenaLC about 2 months ago

#52 - img - quality control

Issue - State: closed - Opened by HelenaLC about 2 months ago - 4 comments

#51 - bkg - data types, file formats & data classes

Issue - State: closed - Opened by HelenaLC about 2 months ago - 2 comments

#50 - brainstorm on 17 dec 2024 (mark lukas helena)

Pull Request - State: closed - Opened by markrobinsonuzh about 2 months ago

#49 - initialize imaging-based ST part

Pull Request - State: closed - Opened by HelenaLC 5 months ago - 2 comments

#47 - render fails: questionable use of here() in analysis-steps.qmd

Issue - State: closed - Opened by vjcitn 9 months ago - 2 comments

#46 - render fails: multiple entries in ExperimentHub

Issue - State: closed - Opened by vjcitn 9 months ago - 3 comments

#45 - make SPE object

Issue - State: closed - Opened by prummer over 1 year ago - 2 comments

#44 - Spatial clustering example using BayesSpace

Issue - State: closed - Opened by lmweber over 1 year ago - 1 comment

#43 - Workflow chapter using Xenium dataset

Issue - State: closed - Opened by lmweber over 1 year ago - 1 comment
Labels: workflow

#42 - Workflow chapter using Visium breast cancer dataset

Issue - State: closed - Opened by lmweber over 1 year ago - 4 comments
Labels: workflow

#41 - Background on technological platforms

Issue - State: closed - Opened by lmweber almost 2 years ago

#40 - Ch 2: Sequencing Prep Overview Figure is Confusing

Issue - State: closed - Opened by berniejmulvey almost 2 years ago - 1 comment

#38 - Small error in Ch. 12.3: PCA

Issue - State: closed - Opened by kinnaryshah over 2 years ago - 2 comments

#37 - Multiple samples / batch effects

Issue - State: closed - Opened by lmweber over 2 years ago - 1 comment

#36 - More background / intro material on scientific context

Issue - State: closed - Opened by lmweber over 2 years ago - 2 comments

#35 - QC metrics: mitochondrial proportion

Issue - State: closed - Opened by lmweber over 2 years ago

#34 - Editorial Suggestions of Chapter 9 Quality Control

Issue - State: closed - Opened by boyiguo1 over 2 years ago - 1 comment

#33 - Reverse dependencies table

Issue - State: closed - Opened by lmweber over 2 years ago

#32 - Logcounts

Issue - State: closed - Opened by lmweber over 2 years ago

#31 - Part IDs

Issue - State: closed - Opened by lmweber over 2 years ago

#30 - QC gene filtering: keep only protein-coding genes

Issue - State: closed - Opened by lmweber over 2 years ago - 1 comment

#29 - Plotting with ST data (not visium)

Issue - State: closed - Opened by ZheFrench almost 3 years ago - 1 comment

#27 - spatial.libd.org is only available via http, not https

Pull Request - State: closed - Opened by lcolladotor over 3 years ago

#26 - scry deviance residuals

Issue - State: closed - Opened by lmweber over 3 years ago

#25 - Preprocessing with alevin-fry

Issue - State: closed - Opened by lmweber over 3 years ago - 1 comment

#24 - Add workflow chapter on a cancer dataset

Issue - State: closed - Opened by lmweber over 3 years ago

#23 - Set up method comparison chapters

Issue - State: closed - Opened by lmweber over 3 years ago