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bio-chipseq-peak-calling

Reference examples tested with: MACS2 2.2+, MACS3 3.0+ Before using code patterns, verify installed versions match. If versions differ: CLI: <tool> --...

by FreedomIntelligence

github 3 files

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+, samtools 1.19+ Before using co...

by FreedomIntelligence

github 5 files

bio-clinical-databases-dbsnp-queries

Reference examples tested with: BioPython 1.83+, Entrez Direct 21.0+ Before using code patterns, verify installed versions match. If versions differ: ...

by FreedomIntelligence

github 3 files

bio-clinical-databases-gnomad-frequencies

Reference examples tested with: requests 2.31+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: Python: p...

by FreedomIntelligence

github 3 files

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, verify installed versions match. ...

by FreedomIntelligence

github 3 files

bio-clinical-databases-myvariant-queries

Reference examples tested with: SnpEff 5.2+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: Python: pip ...

by FreedomIntelligence

github 3 files

bio-clinical-databases-pharmacogenomics

Reference examples tested with: pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: Python: pip show <package...

by FreedomIntelligence

github 3 files

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, verify installed versions match. If...

by FreedomIntelligence

github 4 files

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 versions match. If versions di...

by FreedomIntelligence

github 3 files

bio-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 \ --FDR 0.05 \ --superlocal clippe...

by FreedomIntelligence

github 3 files

bio-clip-seq-clip-preprocessing

umitools extract \ --stdin=readsR1.fastq.gz \ --read2-in=readsR2.fastq.gz \ --bc-pattern=NNNNNNNNNN \ --stdout=R1umi.fastq.gz \ --read2-out=R2umi.fast...

by FreedomIntelligence

github 3 files

bio-comparative-genomics-ancestral-reconstruction

'''Ancestral sequence reconstruction with PAML codeml/baseml''' import subprocess import re from Bio import SeqIO from Bio.Seq import Seq def createas...

by FreedomIntelligence

github 3 files