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14810 skills availablebio-sra-data
Download raw sequencing data from the Sequence Read Archive using the SRA toolkit. brew install sratoolkit sudo apt inst...
bio-splicing-quantification
Reference examples tested with: kallisto 0.50+, pandas 2.2+ Before using code patterns, verify installed versions match....
bio-splicing-pipeline
Complete workflow from raw RNA-seq to differential splicing results. FASTQ → Read QC → STAR 2-pass → Junction QC → rMATS...
bio-spatial-transcriptomics-spatial-visualization
Reference examples tested with: matplotlib 3.8+, numpy 1.26+, scanpy 1.10+, squidpy 1.3+ Before using code patterns, ver...
bio-spatial-transcriptomics-spatial-proteomics
Reference examples tested with: anndata 0.10+, scanpy 1.10+, squidpy 1.3+ Before using code patterns, verify installed v...
bio-spatial-transcriptomics-spatial-neighbors
Reference examples tested with: matplotlib 3.8+, numpy 1.26+, scanpy 1.10+, scikit-learn 1.4+, scipy 1.12+, squidpy 1.3+...
bio-spatial-transcriptomics-spatial-multiomics
Reference examples tested with: Cellpose 3.0+, matplotlib 3.8+, numpy 1.26+, scanpy 1.10+, scipy 1.12+, spatialdata 0.1+...
bio-spatial-transcriptomics-spatial-data-io
Reference examples tested with: anndata 0.10+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, spatialdata 0.1+, squidpy 1.3+ Be...
bio-small-rna-seq-smrna-preprocessing
Small RNA libraries have specific 3' adapters that must be removed: cutadapt \ -a TGGAATTCTCGGGTGCCAAGG \ -m 18 \ -M 30 ...
bio-small-rna-seq-mirdeep2-analysis
Collapsed reads (FASTA) mapper.pl ---------> Align to genome, create ARF file miRDeep2.pl -------> Predict novel miRNAs,...
bio-single-cell-trajectory-inference
Reference examples tested with: Cell Ranger 8.0+, scanpy 1.10+ Before using code patterns, verify installed versions mat...
bio-single-cell-scatac-analysis
Reference examples tested with: MACS2 2.2+, scanpy 1.10+ Before using code patterns, verify installed versions match. If...
bio-single-cell-metabolite-communication
Reference examples tested with: matplotlib 3.8+, scanpy 1.10+ Before using code patterns, verify installed versions matc...
bio-single-cell-doublet-detection
Reference examples tested with: matplotlib 3.8+, numpy 1.26+, scanpy 1.10+ Before using code patterns, verify installed ...
bio-single-cell-clustering
Reference examples tested with: ggplot2 3.5+, matplotlib 3.8+, scanpy 1.10+ Before using code patterns, verify installed...
bio-single-cell-cell-communication
Reference examples tested with: ggplot2 3.5+, scanpy 1.10+ Before using code patterns, verify installed versions match. ...
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 patter...
bio-sequence-statistics
Reference examples tested with: BioPython 1.83+, samtools 1.19+ Before using code patterns, verify installed versions ma...
bio-sequence-similarity
Advanced methods for finding homologous sequences beyond standard BLAST. Builds a position-specific scoring matrix (PSSM...
bio-sequence-properties
Calculate physical and chemical properties of biological sequences using Biopython. from Bio.Seq import Seq from Bio.Seq...
bio-seq-objects
Create and manipulate biological sequence objects using Biopython. from Bio.Seq import Seq, MutableSeq from Bio.SeqRecor...
bio-sam-bam-basics
View and convert alignment files using samtools and pysam. | Format | Description | Use Case | |--------|-------------|-...
bio-rna-quantification-alignment-free-quant
Quantify transcript abundance directly from FASTQ reads using pseudo-alignment (kallisto) or selective alignment (Salmon...
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, verif...