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bio-proteomics-differential-abundance

Reference examples tested with: R stats (base), ggplot2 3.5+, limma 3.58+, numpy 1.26+, pandas 2.2+, scipy 1.12+, statsmodels 0.14+ Before using code ...

by FreedomIntelligence

github 3 files

bio-proteomics-protein-inference

Reference examples tested with: pyOpenMS 3.1+ Before using code patterns, verify installed versions match. If versions differ: Python: pip show <packa...

by FreedomIntelligence

github 3 files

bio-proteomics-quantification

Reference examples tested with: MSnbase 2.28+, numpy 1.26+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions diffe...

by FreedomIntelligence

github 3 files

bio-reaction-enumeration

Reference examples tested with: RDKit 2024.03+ Before using code patterns, verify installed versions match. If versions differ: Python: pip show <pack...

by FreedomIntelligence

github 3 files

bio-read-alignment-bowtie2-alignment

bowtie2-build reference.fa referenceindex bowtie2-build --threads 8 reference.fa referenceindex bowtie2 -p 8 -x referenceindex -1 reads1.fq.gz -2 read...

by FreedomIntelligence

github 3 files

bio-read-alignment-star-alignment

STAR --runMode genomeGenerate \ --runThreadN 8 \ --genomeDir starindex/ \ --genomeFastaFiles reference.fa \ --sjdbGTFfile annotation.gtf \ --sjdbOverh...

by FreedomIntelligence

github 3 files

bio-read-qc-quality-filtering

Reference examples tested with: Trimmomatic 0.39+, cutadapt 4.4+, fastp 0.23+ Before using code patterns, verify installed versions match. If versions...

by FreedomIntelligence

github 3 files

bio-read-qc-umi-processing

Reference examples tested with: pandas 2.2+, samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: Python: p...

by FreedomIntelligence

github 3 files

bio-read-sequences

Reference examples tested with: BioPython 1.83+ Before using code patterns, verify installed versions match. If versions differ: Python: pip show biop...

by FreedomIntelligence

github 11 files

bio-reporting-figure-export

import matplotlib.pyplot as plt plt.rcParams.update({ 'font.size': 8, 'font.family': 'Arial', 'axes.linewidth': 0.5, 'lines.linewidth': 1, 'figure.dpi...

by FreedomIntelligence

github 3 files

bio-reporting-quarto-reports

--- title: "Analysis Report" author: "Your Name" date: today format: html: toc: true code-fold: true theme: cosmo --- --- title: "scRNA-seq Analysis" ...

by FreedomIntelligence

github 4 files

bio-reporting-rmarkdown-reports

--- title: "RNA-seq Analysis Report" author: "Your Name" date: "r Sys.Date()" output: htmldocument: toc: true tocfloat: true codefolding: hide theme: ...

by FreedomIntelligence

github 3 files