Individual skill
knn-imputation
Use when filtering genes with high missingness and then imputing missing values in a bulk expression matrix with group-aware KNN through DMwR2, where donor samples are restricted by one annotation column before imputation. For strata with 10 or fewer samples, the script falls back to row-wise direct filling with mean or median. NOT for: single-cell data, multi-column stratification, non-tabular inputs, network access, or interactive workflows.
awesome-med-research-skills/Data Analysis/knn-imputation/SKILL.md
Source commit 686e09dfdb45d9fa1a08664f06bb93769b3c9d91
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- Last checked
- Nov 9, 2026
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- Repository last updated
- Sep 17, 2026
- License
- MIT
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- bioinformatics Repository topic
- computational-biology Repository topic
- data-analysis Repository topic
- ai Repository topic
- biology Repository topic
- cancer-genomics Repository topic
- data-visualization Repository topic
- differential-expression Repository topic
- genomics Repository topic
- medical Repository topic
- engineering Derived category
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SKILL.mdcore · 9,981 bytesSKILL.mdcore · 9,981 bytesSKILL.mdcore · 9,981 bytesSKILL.mdcore · 9,981 bytesSKILL.mdcore · 9,981 bytesSKILL.mdcore · 9,981 bytesSKILL.mdcore · 9,981 byteseval_report_knn-imputation_result.jsonasset · 15,339 bytesreferences/algorithm.mddoc · 3,556 bytesreferences/cli-guide.mddoc · 4,108 bytesreferences/troubleshooting.mddoc · 3,122 bytesscripts/functions.Rasset · 4,266 bytesscripts/imputation_functions.Rasset · 5,095 bytesscripts/imputation_helpers.Rasset · 3,016 bytesscripts/main.Rruns · 5,005 bytesscripts/run_analysis.Rasset · 5,561 bytesscripts/utils.Rasset · 4,131 bytestests/data/sample_expression_matrix.csvasset · 7,313,333 bytestests/data/sample_groups.csvasset · 674 bytestests/data/sample_groups_custom.csvasset · 634 bytes
Read excerpt
# KNN Imputation
## When to Use
Use this skill when you need to remove genes with more than 50% missing values from a bulk expression matrix and then run group-aware KNN imputation, with the donor pool restricted by one grouping column.
Do not use this skill for:
- single-cell data
- multi-column stratification
- non-tabular inputs
- network-dependent workflows
- interactive analysis sessions
## When to Read External Files