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bio-comparative-genomics-hgt-detection
'''HGT detection with HGTector and compositional methods''' import subprocess import pandas as pd import numpy as np from Bio import SeqIO from collec...
bio-comparative-genomics-ortholog-inference
'''Ortholog inference with OrthoFinder''' import subprocess import pandas as pd import os def runorthofinder(proteomedir, outputdir=None, threads=4): ...
bio-comparative-genomics-synteny-analysis
'''Synteny analysis with MCScanX and visualization''' import subprocess import pandas as pd from collections import defaultdict def preparemcscanxinpu...
bio-consensus-sequences
Reference examples tested with: BioPython 1.83+, bcftools 1.19+, bedtools 2.31+, minimap2 2.26+, samtools 1.19+ Before using code patterns, verify ins...
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, verify installed versions match....
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 using code patterns, verify i...
bio-crispr-screens-base-editing-analysis
Reference examples tested with: CRISPResso2 2.2+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: Python:...
bio-crispr-screens-crispresso-editing
Reference examples tested with: CRISPResso2 2.2+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: Python:...
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, verify installed versions match. If...
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+ Before using code patterns, v...
bio-data-visualization-genome-tracks
cat > tracks.ini << 'EOF' [bigwig] file = coverage.bw title = Coverage height = 4 color = #4DBBD5 minvalue = 0 [spacer] height = 0.5 [peaks] file = pe...
bio-data-visualization-ggplot2-fundamentals
library(ggplot2) ggplot(data, aes(x = var1, y = var2)) + geompoint() ggplot(df, aes(x, y)) + geompoint() ggplot(df, aes(x, y)) + geomline() ggplot(df,...