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14810 skills availablebio-clip-seq-clip-peak-calling
clipper \ -b deduped.bam \ -s hg38 \ -o peaks.bed \ --save-pickle clipper \ -b deduped.bam \ -s hg38 \ -o peaks.bed \ --...
bio-clinical-databases-tumor-mutational-burden
Reference examples tested with: Ensembl VEP 111+, SnpEff 5.2+, pandas 2.2+ Before using code patterns, verify installed ...
bio-clinical-databases-polygenic-risk
Reference examples tested with: LDpred2 1.14+, PRSice-2 2.3+, numpy 1.26+, scipy 1.12+ Before using code patterns, verif...
bio-clinical-databases-pharmacogenomics
Reference examples tested with: pandas 2.2+ Before using code patterns, verify installed versions match. If versions dif...
bio-clinical-databases-myvariant-queries
Reference examples tested with: SnpEff 5.2+, pandas 2.2+ Before using code patterns, verify installed versions match. If...
bio-clinical-databases-hla-typing
Reference examples tested with: OptiType 1.3+, STAR 2.7.11+, pandas 2.2+, samtools 1.19+ Before using code patterns, ver...
bio-clinical-databases-gnomad-frequencies
Reference examples tested with: requests 2.31+, pandas 2.2+ Before using code patterns, verify installed versions match....
bio-clinical-databases-dbsnp-queries
Reference examples tested with: BioPython 1.83+, Entrez Direct 21.0+ Before using code patterns, verify installed versio...
bio-chipseq-qc
Reference examples tested with: MACS3 3.0+, Subread 2.0+, bedtools 2.31+, deepTools 3.5+, pybedtools 0.9+, pysam 0.22+, ...
bio-chipseq-peak-calling
Reference examples tested with: MACS2 2.2+, MACS3 3.0+ Before using code patterns, verify installed versions match. If v...
bio-chipseq-peak-annotation
Reference examples tested with: MACS3 3.0+, clusterProfiler 4.10+ Before using code patterns, verify installed versions ...
bio-cfdna-preprocessing
Reference examples tested with: BWA 0.7.17+, fgbio 2.1+, matplotlib 3.8+, numpy 1.26+, pysam 0.22+, samtools 1.19+ Befor...
bio-causal-genomics-mendelian-randomization
Reference examples tested with: TwoSampleMR 0.5+, MendelianRandomization 0.9+ Before using code patterns, verify install...
bio-causal-genomics-mediation-analysis
Reference examples tested with: R stats (base), ggplot2 3.5+ Before using code patterns, verify installed versions match...
bio-causal-genomics-fine-mapping
Reference examples tested with: ggplot2 3.5+ Before using code patterns, verify installed versions match. If versions di...
bio-batch-downloads
Download large numbers of records from NCBI efficiently using the history server, batching, and proper rate limiting. fr...
bio-basecalling
Reference examples tested with: samtools 1.19+ Before using code patterns, verify installed versions match. If versions ...
bio-atac-seq-nucleosome-positioning
Reference examples tested with: Rsamtools 2.18+, matplotlib 3.8+, numpy 1.26+, pyBigWig 0.3+, pysam 0.22+, samtools 1.19...
bio-atac-seq-differential-accessibility
Reference examples tested with: DESeq2 1.42+, GenomicRanges 1.54+, Subread 2.0+, numpy 1.26+, pandas 2.2+, scanpy 1.10+,...
bio-atac-seq-atac-peak-calling
Reference examples tested with: Bowtie2 2.5.3+, MACS3 3.0+, samtools 1.19+ Before using code patterns, verify installed ...
bio-alignment-validation
Post-alignment quality control to verify alignment quality and identify issues. Insert size should match library prepara...
bio-alignment-sorting
Sort alignment files by coordinate or read name using samtools and pysam. | Order | Flag | Use Case | |-------|------|--...
bio-alignment-pairwise
Reference examples tested with: BioPython 1.83+ Before using code patterns, verify installed versions match. If versions...
bio-alignment-msa-statistics
Reference examples tested with: BioPython 1.83+, numpy 1.26+ Before using code patterns, verify installed versions match...