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bio-data-visualization-interactive-visualization

import plotly.express as px import plotly.graphobjects as go import pandas as pd fig = px.scatter(df, x='PC1', y='PC2', color='condition', hoverdata=[...

by FreedomIntelligence

github 3 files

bio-data-visualization-multipanel-figures

library(patchwork) p1 <- ggplot(df, aes(x, y)) + geompoint() p2 <- ggplot(df, aes(group, value)) + geomboxplot() p3 <- ggplot(df, aes(x)) + geomhistog...

by FreedomIntelligence

github 4 files

bio-de-edger-basics

Reference examples tested with: DESeq2 1.42+, edgeR 4.0+, limma 3.58+, scanpy 1.10+ Before using code patterns, verify installed versions match. If ve...

by FreedomIntelligence

github 5 files

bio-differential-expression-timeseries-de

Reference examples tested with: DESeq2 1.42+, edgeR 4.0+, ggplot2 3.5+, limma 3.58+, scanpy 1.10+ Before using code patterns, verify installed version...

by FreedomIntelligence

github 3 files

bio-differential-splicing

Reference examples tested with: STAR 2.7.11+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: Python: pip...

by FreedomIntelligence

github 4 files

bio-entrez-fetch

Retrieve records from NCBI databases using Biopython's Entrez module (EFetch, ESummary utilities). from Bio import Entrez Entrez.email = 'your.email@e...

by FreedomIntelligence

github 5 files

bio-entrez-link

Navigate between NCBI databases using Biopython's Entrez module (ELink utility). from Bio import Entrez Entrez.email = 'your.email@example.com' # Req...

by FreedomIntelligence

github 5 files

bio-epidemiological-genomics-amr-surveillance

Reference examples tested with: AMRFinderPlus 3.12+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: Pyth...

by FreedomIntelligence

github 3 files

bio-epidemiological-genomics-phylodynamics

Reference examples tested with: BioPython 1.83+, TreeTime 0.11+, scanpy 1.10+ Before using code patterns, verify installed versions match. If versions...

by FreedomIntelligence

github 3 files

bio-epidemiological-genomics-transmission-inference

Reference examples tested with: BioPython 1.83+, TreeTime 0.11+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scanpy 1.10+ Before using code patterns, v...

by FreedomIntelligence

github 3 files

bio-epitranscriptomics-m6a-peak-calling

library(exomePeak2) result <- exomePeak2( bamip = c('IPrep1.bam', 'IPrep2.bam'), baminput = c('Inputrep1.bam', 'Inputrep2.bam'), gff = 'genes.gtf', ge...

by FreedomIntelligence

github 4 files

bio-epitranscriptomics-modification-visualization

library(Guitar) library(TxDb.Hsapiens.UCSC.hg38.knownGene) peaks <- import('m6apeaks.bed') GuitarPlot( peaks, txdb = TxDb.Hsapiens.UCSC.hg38.knownGene...

by FreedomIntelligence

github 4 files