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14810 skills availablebio-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+...
bio-epidemiological-genomics-phylodynamics
Reference examples tested with: BioPython 1.83+, TreeTime 0.11+, scanpy 1.10+ Before using code patterns, verify install...
bio-epidemiological-genomics-amr-surveillance
Reference examples tested with: AMRFinderPlus 3.12+, pandas 2.2+ Before using code patterns, verify installed versions m...
bio-entrez-link
Navigate between NCBI databases using Biopython's Entrez module (ELink utility). from Bio import Entrez Entrez.email = '...
bio-entrez-fetch
Retrieve records from NCBI databases using Biopython's Entrez module (EFetch, ESummary utilities). from Bio import Entre...
bio-differential-splicing
Reference examples tested with: STAR 2.7.11+, pandas 2.2+ Before using code patterns, verify installed versions match. I...
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 patt...
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 i...
bio-data-visualization-multipanel-figures
library(patchwork) p1 <- ggplot(df, aes(x, y)) + geompoint() p2 <- ggplot(df, aes(group, value)) + geomboxplot() p3 <- g...
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', ...
bio-data-visualization-ggplot2-fundamentals
library(ggplot2) ggplot(data, aes(x = var1, y = var2)) + geompoint() ggplot(df, aes(x, y)) + geompoint() ggplot(df, aes(...
bio-data-visualization-genome-tracks
cat > tracks.ini << 'EOF' [bigwig] file = coverage.bw title = Coverage height = 4 color = #4DBBD5 minvalue = 0 [spacer] ...
bio-crispr-screens-screen-qc
Reference examples tested with: MAGeCK 0.5+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scikit-learn 1.4+, seaborn 0.13+...
bio-crispr-screens-library-design
Reference examples tested with: BioPython 1.83+, MAGeCK 0.5+, numpy 1.26+, pandas 2.2+ Before using code patterns, verif...
bio-crispr-screens-crispresso-editing
Reference examples tested with: CRISPResso2 2.2+, pandas 2.2+ Before using code patterns, verify installed versions matc...
bio-crispr-screens-base-editing-analysis
Reference examples tested with: CRISPResso2 2.2+, pandas 2.2+ Before using code patterns, verify installed versions matc...
bio-copy-number-cnv-visualization
Reference examples tested with: GATK 4.5+, ggplot2 3.5+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, seaborn 0.13+ Before...
bio-copy-number-cnv-annotation
Reference examples tested with: bedtools 2.31+, pandas 2.2+, pybedtools 0.9+, pysam 0.22+ Before using code patterns, ve...
bio-consensus-sequences
Reference examples tested with: BioPython 1.83+, bcftools 1.19+, bedtools 2.31+, minimap2 2.26+, samtools 1.19+ Before u...
bio-comparative-genomics-synteny-analysis
'''Synteny analysis with MCScanX and visualization''' import subprocess import pandas as pd from collections import defa...
bio-comparative-genomics-ortholog-inference
'''Ortholog inference with OrthoFinder''' import subprocess import pandas as pd import os def runorthofinder(proteomedir...
bio-comparative-genomics-hgt-detection
'''HGT detection with HGTector and compositional methods''' import subprocess import pandas as pd import numpy as np fro...
bio-comparative-genomics-ancestral-reconstruction
'''Ancestral sequence reconstruction with PAML codeml/baseml''' import subprocess import re from Bio import SeqIO from B...
bio-clip-seq-clip-preprocessing
umitools extract \ --stdin=readsR1.fastq.gz \ --read2-in=readsR2.fastq.gz \ --bc-pattern=NNNNNNNNNN \ --stdout=R1umi.fas...