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dask
Dask is a Python library for parallel and distributed computing that enables three critical capabilities: Larger-than-memory execution on single machi...
bio-atac-seq-motif-deviation
Reference examples tested with: ggplot2 3.5+, limma 3.58+ Before using code patterns, verify installed versions match. If versions differ: R: packageV...
bio-expression-matrix-metadata-joins
import pandas as pd metadata = pd.readcsv('sampleinfo.csv', indexcol=0) import pandas as pd counts = pd.readcsv('counts.tsv', sep='\t', indexcol=0) me...
bio-reporting-automated-qc-reports
multiqc results/ -o qcreport/ multiqc results/ -n myprojectqc multiqc results/ --module fastqc --module star MultiQC recognizes outputs from 100+ bioi...
bio-liquid-biopsy-pipeline
Complete workflow for cfDNA analysis from sequencing to clinical interpretation. Pre-analytical QC → cfDNA Preprocessing → Fragment QC ┌──────────────...
bio-data-visualization-heatmaps-clustering
library(pheatmap) library(RColorBrewer) pheatmap(mat, scale = 'row', clusterrows = TRUE, clustercols = TRUE) annotationcol <- data.frame( Condition = ...
bio-geo-data
Query and access Gene Expression Omnibus datasets using Biopython's Entrez module. from Bio import Entrez Entrez.email = 'your.email@example.com' # R...
bio-ribo-seq-orf-detection
Reference examples tested with: BioPython 1.83+, DESeq2 1.42+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions di...
varCADD
Genome-wide pathogenicity prediction leveraging standing variation data to improve accuracy over traditional CADD scores. Variant Prioritization: Rank...
jaspar-database
JASPAR (https://jaspar.elixir.no/) is the gold-standard open-access database of curated, non-redundant transcription factor (TF) binding profiles stor...
bio-phylo-tree-visualization
Draw phylogenetic trees using matplotlib integration. from Bio import Phylo import matplotlib.pyplot as plt tree = Phylo.read('tree.nwk', 'newick') pr...
image-analysis
Extract features and segment tissue images in spatial transcriptomics data. import squidpy as sq import scanpy as sc import numpy as np import matplot...