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bio-experimental-design-batch-design
Batch effects are unavoidable. Good design makes them correctable. Never confound batch with condition - Each batch must contain all conditions Balanc...
bio-experimental-design-multiple-testing
Testing 20,000 genes at p < 0.05 yields 1,000 false positives by chance. Correction is essential. padj <- p.adjust(pvalues, method = 'bonferroni') pad...
bio-experimental-design-power-analysis
Power = probability of detecting a true effect. Underpowered studies waste resources; overpowered studies are inefficient. library(RNASeqPower) rnapow...
bio-expression-matrix-counts-ingest
import pandas as pd counts = pd.readcsv('counts.tsv', sep='\t', indexcol=0) counts = pd.readcsv('counts.csv', indexcol=0) counts = pd.readcsv('counts....
bio-expression-matrix-gene-id-mapping
import mygene import pandas as pd mg = mygene.MyGeneInfo() ensemblids = ['ENSG00000141510', 'ENSG00000012048', 'ENSG00000141736'] results = mg.queryma...
bio-flow-cytometry-bead-normalization
Reference examples tested with: flowCore 2.14+, ggplot2 3.5+ Before using code patterns, verify installed versions match. If versions differ: R: packa...
bio-flow-cytometry-cytometry-qc
Reference examples tested with: flowCore 2.14+, ggplot2 3.5+ Before using code patterns, verify installed versions match. If versions differ: R: packa...
bio-flow-cytometry-doublet-detection
Reference examples tested with: flowCore 2.14+, ggplot2 3.5+ Before using code patterns, verify installed versions match. If versions differ: R: packa...
bio-flow-cytometry-fcs-handling
Reference examples tested with: flowCore 2.14+, scanpy 1.10+ Before using code patterns, verify installed versions match. If versions differ: R: packa...
bio-flow-cytometry-gating-analysis
Reference examples tested with: flowCore 2.14+ Before using code patterns, verify installed versions match. If versions differ: R: packageVersion('<pk...
bio-format-conversion
Reference examples tested with: BioPython 1.83+, samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: Pytho...
bio-genome-assembly-contamination-detection
checkm2 predict --input assembly.fa --output-directory checkm2output --threads 16 checkm2 predict --input genomes/ --output-directory checkm2output \ ...