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bio-research-tools-biomarker-signature-studio
Design validated biomarker panels that are explainable, stable, and ready for translational follow-up. This skill stitches together the existing bioma...
bio-restriction-enzyme-selection
from Bio import SeqIO from Bio.Restriction import Analysis, CommOnly, AllEnzymes record = SeqIO.read('sequence.fasta', 'fasta') seq = record.seq analy...
bio-reverse-complement
Generate complementary and reverse complementary sequences using Biopython. from Bio.Seq import Seq Returns the reverse complement (5' to 3' of the op...
bio-ribo-seq-ribosome-periodicity
Reference examples tested with: matplotlib 3.8+, numpy 1.26+, pysam 0.22+, scipy 1.12+ Before using code patterns, verify installed versions match. If...
bio-rna-quantification-alignment-free-quant
Quantify transcript abundance directly from FASTQ reads using pseudo-alignment (kallisto) or selective alignment (Salmon). salmon index -t transcripts...
bio-sam-bam-basics
View and convert alignment files using samtools and pysam. | Format | Description | Use Case | |--------|-------------|----------| | SAM | Text format...
bio-seq-objects
Create and manipulate biological sequence objects using Biopython. from Bio.Seq import Seq, MutableSeq from Bio.SeqRecord import SeqRecord The basic s...
bio-sequence-properties
Calculate physical and chemical properties of biological sequences using Biopython. from Bio.Seq import Seq from Bio.SeqUtils import gcfraction, molec...
bio-sequence-similarity
Advanced methods for finding homologous sequences beyond standard BLAST. Builds a position-specific scoring matrix (PSSM) through iterations to find d...
bio-sequence-statistics
Reference examples tested with: BioPython 1.83+, samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: Pytho...
bio-single-cell-batch-integration
Reference examples tested with: anndata 0.10+, scanpy 1.10+, scikit-learn 1.4+, scvi-tools 1.1+ Before using code patterns, verify installed versions ...
bio-single-cell-cell-communication
Reference examples tested with: ggplot2 3.5+, scanpy 1.10+ Before using code patterns, verify installed versions match. If versions differ: Python: pi...