nf-core/spatialaxe
View on GitHubA bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data
- Stars
- 46
- Forks
- 23
- Open beginner issues
- 0
- Indexed issues
- 48
- Dominant language
- Python
- License
- MIT
- Last GitHub push
- Aug 6, 2026
- Latest indexed
- Sep 19, 2026
- Contributing guide
- Contributing guide
- Code of conduct
- Code of conduct
- Beginner labels
- No beginner labels indexed
- PR merge metrics
- No merged PRs in 30d
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enhancement prio3
Difficulty 5/5 Over a week Newbie friendliness 25/100
nf-core/spatialaxe#211 ·
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enhancement prio1
Difficulty 3/5 1-2 days Newbie friendliness 48/100
nf-core/spatialaxe#209 ·
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enhancement prio1
Difficulty 5/5 Over a week Newbie friendliness 20/100
nf-core/spatialaxe#208 ·
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enhancement prio2
Difficulty 3/5 1-2 days Newbie friendliness 52/100
nf-core/spatialaxe#207 ·
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enhancement
Difficulty 3/5 1-2 days Newbie friendliness 58/100
nf-core/spatialaxe#187 ·
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enhancement prio1
Difficulty 4/5 3-5 days Newbie friendliness 45/100
nf-core/spatialaxe#185 ·
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[add] bento tools Openenhancement
nf-core/spatialaxe#181 · 1 assignee ·
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enhancement prio1
nf-core/spatialaxe#179 · 1 assignee ·
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enhancement prio1
nf-core/spatialaxe#178 · 1 assignee ·
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[update] Base config Openenhancement prio1
Difficulty 5/5 Over a week Newbie friendliness 25/100
nf-core/spatialaxe#177 ·
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enhancement prio2
Difficulty 4/5 3-5 days Newbie friendliness 25/100
nf-core/spatialaxe#176 · 1 comment ·
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enhancement prio2
Difficulty 4/5 3-5 days Newbie friendliness 38/100
nf-core/spatialaxe#175 ·
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enhancement prio2
nf-core/spatialaxe#174 · 1 assignee ·
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Difficulty 2/5 Half a day Newbie friendliness 76/100
nf-core/spatialaxe#169 ·
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Difficulty 4/5 3-5 days Newbie friendliness 35/100
nf-core/spatialaxe#168 · 1 reaction ·
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Difficulty 4/5 3-5 days Newbie friendliness 52/100
nf-core/spatialaxe#167 ·
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Difficulty 4/5 3-5 days Newbie friendliness 48/100
nf-core/spatialaxe#166 ·
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[upgrade] Baysor: migrate Julia v0.7.1 → C++ cpp-0.8.2 (eliminates PARQUET_TO_CSV for Baysor paths) Open
Difficulty 5/5 Over a week Newbie friendliness 35/100
nf-core/spatialaxe#164 ·
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Difficulty 5/5 Over a week Newbie friendliness 45/100
nf-core/spatialaxe#165 ·
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bug
Difficulty 5/5 Over a week Newbie friendliness 35/100
nf-core/spatialaxe#163 ·
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bug
Difficulty 3/5 1-2 days Newbie friendliness 35/100
nf-core/spatialaxe#161 ·
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enhancement
Difficulty 5/5 Over a week Newbie friendliness 38/100
nf-core/spatialaxe#157 ·
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[add] DenoIST Openmodule prio3 qc
nf-core/spatialaxe#128 · 1 assignee ·
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module prio3 qc
Difficulty 4/5 3-5 days Newbie friendliness 25/100
nf-core/spatialaxe#127 ·
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[add] module SCS Openmodule qc segmentation
nf-core/spatialaxe#126 · 1 assignee ·
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[add] module Bering Openlots-of-work module segmentation
Difficulty 5/5 Over a week Newbie friendliness 25/100
nf-core/spatialaxe#125 ·
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module prio3 qc
Difficulty 4/5 3-5 days Newbie friendliness 35/100
nf-core/spatialaxe#124 ·
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enhancement prio2
nf-core/spatialaxe#120 · 1 assignee ·
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[add] module troutpy Openmodule prio3 qc
Difficulty 4/5 3-5 days Newbie friendliness 30/100
nf-core/spatialaxe#119 ·
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[add] module SeqTraq Openmodule prio3 qc
nf-core/spatialaxe#117 · 1 assignee ·
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bug
Difficulty 4/5 3-5 days Newbie friendliness 15/100
nf-core/spatialaxe#116 ·
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bug
nf-core/spatialaxe#115 · 1 comment · 1 assignee ·
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enhancement
nf-core/spatialaxe#110 · 1 assignee ·
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enhancement
nf-core/spatialaxe#104 · 1 assignee ·
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metadata module prio3
nf-core/spatialaxe#66 · 1 assignee ·
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[add] module grandqc Openmodule prio3 qc testing
nf-core/spatialaxe#60 · 1 comment · 1 assignee ·
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enhancement
nf-core/spatialaxe#59 · 1 comment · 1 assignee ·
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[add] module ResolVI Openmodule prio3 qc
Difficulty 5/5 Over a week Newbie friendliness 25/100
nf-core/spatialaxe#51 ·
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module prio3 segmentation
Difficulty 5/5 Over a week Newbie friendliness 25/100
nf-core/spatialaxe#42 ·
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[add] module Vista2D Openmetadata module prio3
Difficulty 5/5 Over a week Newbie friendliness 25/100
nf-core/spatialaxe#38 · 1 comment ·
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module prio3 segmentation
Difficulty 5/5 Over a week Newbie friendliness 20/100
nf-core/spatialaxe#35 ·
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lots-of-work metadata module prio3
nf-core/spatialaxe#26 · 1 assignee ·
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enhancement prio3
Difficulty 5/5 Over a week Newbie friendliness 20/100
nf-core/spatialaxe#25 ·
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enhancement prio3
Difficulty 5/5 Over a week Newbie friendliness 25/100
nf-core/spatialaxe#24 ·
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enhancement prio3
nf-core/spatialaxe#22 · 1 assignee ·
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[add] module BIDCell Openmodule prio3 segmentation
Difficulty 5/5 Over a week Newbie friendliness 25/100
nf-core/spatialaxe#17 · 3 comments ·
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[add] module QuPath Openmodule prio2
nf-core/spatialaxe#9 · 5 comments · 1 assignee ·
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module prio2 testing
nf-core/spatialaxe#7 · 1 assignee ·