Research & Science · pysam

Soft- or hard-clips PCR primer footprints from aligned amplicon BAMs so primer bases stop masquerading as confirmed reference sequence.

GPTomics/bioSkills

Filters BAM alignments by FLAG bits, mapping quality and regions with samtools view or pysam, with recipes for common keep and drop cases.

GPTomics/bioSkills

Genomic file toolkit. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam.

GPTomics/bioSkills

Sort alignment files by coordinate or read name using samtools and pysam.

GPTomics/bioSkills

Provides Python/HTSlib workflows for genomic files. An agent skill from K-Dense-AI/scientific-agent-skills.

K-Dense-AI/scientific-agent-skills

Omics and single-cell workflow guide for AnnData, Scanpy-style dataset profiling, PyDESeq2-oriented count checks, pysam alignment inspection, and pyOpenMS mass-spectrometry summaries.

DrugClaw/DrugClaw

Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content.

GPTomics/bioSkills

Mark and remove PCR/optical duplicates using samtools fixmate and markdup.

GPTomics/bioSkills

Generate consensus sequences and manage reference files using samtools.

GPTomics/bioSkills

View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam.

GPTomics/bioSkills

Generate pileup data for variant calling using samtools mpileup and pysam.

GPTomics/bioSkills

Production-ready genomics and epigenomics data processing for BixBench questions.

wu-yc/LabClaw

Detects somatic mutations in circulating tumor DNA, treating low-VAF detection as a signal-versus-noise problem set by error suppression and molecules sampled, not by the choice of caller.

GPTomics/bioSkills

ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discovery Rate) for replicate…

FreedomIntelligence/OpenClaw-Medical-Skills

Assesses RNA-seq data quality for splicing analysis including junction saturation curves, splice site strength scoring, and junction coverage metrics using RSeQC.

FreedomIntelligence/OpenClaw-Medical-Skills

Biopython sequence analysis: parse FASTA/FASTQ/GenBank/GFF (SeqIO), NCBI Entrez (esearch/efetch/elink), remote/local BLAST, pairwise/MSA alignment (PairwiseAligner, MUSCLE/ClustalW), phylogenetic…

jaechang-hits/SciAgent-Skills

CLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments.

jaechang-hits/SciAgent-Skills

Genomic file toolkit. An agent skill from aipoch/medical-research-skills.

aipoch/medical-research-skills

Read/write SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills