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bio-alignment-sorting

Sort alignment files by coordinate or read name using samtools and pysam. | Order | Flag | Use Case | |-------|------|----------| | Coordinate | defau...

by FreedomIntelligence

github 3 files

bio-alignment-validation

Post-alignment quality control to verify alignment quality and identify issues. Insert size should match library preparation protocol. samtools stats ...

by FreedomIntelligence

github 4 files

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 versions match. If versions di...

by FreedomIntelligence

github 3 files

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+, scipy 1.12+ Before using code...

by FreedomIntelligence

github 3 files

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+ Before using code patterns, ...

by FreedomIntelligence

github 3 files

bio-basecalling

Reference examples tested with: samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: CLI: <tool> --version ...

by FreedomIntelligence

github 4 files

bio-batch-downloads

Download large numbers of records from NCBI efficiently using the history server, batching, and proper rate limiting. from Bio import Entrez import ti...

by FreedomIntelligence

github 5 files

bio-causal-genomics-fine-mapping

Reference examples tested with: ggplot2 3.5+ Before using code patterns, verify installed versions match. If versions differ: R: packageVersion('<pkg>...

by FreedomIntelligence

github 5 files

bio-causal-genomics-mediation-analysis

Reference examples tested with: R stats (base), ggplot2 3.5+ Before using code patterns, verify installed versions match. If versions differ: R: packa...

by FreedomIntelligence

github 4 files

bio-causal-genomics-mendelian-randomization

Reference examples tested with: TwoSampleMR 0.5+, MendelianRandomization 0.9+ Before using code patterns, verify installed versions match. If versions...

by FreedomIntelligence

github 4 files

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+ Before using code patterns, verify ...

by FreedomIntelligence

github 3 files

bio-chipseq-peak-annotation

Reference examples tested with: MACS3 3.0+, clusterProfiler 4.10+ Before using code patterns, verify installed versions match. If versions differ: R: ...

by FreedomIntelligence

github 3 files