Search
Research & Science · pysam · For researchers
Skills
Sort:BestMost starsTrending todayTrending this weekTrending this monthNewestRecently updatedName
| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 1 | Soft- or hard-clips PCR primer footprints from aligned amplicon BAMs so primer bases stop masquerading as confirmed reference sequence. | GPTomics/ | 1.2k | 2 repos | ~2.2k | Automated safety check: Pass | MIT | 1 mo ago |
| 2 | Filters BAM alignments by FLAG bits, mapping quality and regions with samtools view or pysam, with recipes for common keep and drop cases. | GPTomics/ | 1.2k | 2 repos | ~3.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 3 | 3.Pysam Genomic file toolkit. An agent skill from davila7/claude-code-templates. | davila7/ | 33k | 10 repos | ~2.5k | Automated safety check: Pass | MIT | today |
| 4 | Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. | GPTomics/ | 1.2k | 2 repos | ~2.4k | Automated safety check: Pass | MIT | 1 mo ago |
| 5 | Sort alignment files by coordinate or read name using samtools and pysam. | GPTomics/ | 1.2k | 2 repos | ~2.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 6 | 6.Pysam Provides Python/HTSlib workflows for genomic files. An agent skill from K-Dense-AI/scientific-agent-skills. | K-Dense-AI/ | 48k | 1 repo | ~3.4k | Automated safety check: Notes | MIT | 6 days ago |
| 7 | 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/ | 126 | — | ~1.1k | Automated safety check: Pass | Apache-2.0 | 6 mo ago |
| 8 | Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content. | GPTomics/ | 1.2k | 2 repos | ~3.4k | Automated safety check: Pass | MIT | 1 mo ago |
| 9 | Mark and remove PCR/optical duplicates using samtools fixmate and markdup. | GPTomics/ | 1.2k | 2 repos | ~3.7k | Automated safety check: Pass | MIT | 1 mo ago |
| 10 | Generate consensus sequences and manage reference files using samtools. | GPTomics/ | 1.2k | 2 repos | ~3.1k | Automated safety check: Pass | MIT | 1 mo ago |
| 11 | View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. | GPTomics/ | 1.2k | 2 repos | ~3.7k | Automated safety check: Pass | MIT | 1 mo ago |
| 12 | Generate pileup data for variant calling using samtools mpileup and pysam. | GPTomics/ | 1.2k | 2 repos | ~3.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 13 | Production-ready genomics and epigenomics data processing for BixBench questions. | wu-yc/ | 1.1k | 2 repos | ~14k | Automated safety check: Pass | No licence | 6 mo ago |
| 14 | 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/ | 1.2k | 1 repo | ~5.1k | Automated safety check: Pass | MIT | 1 mo ago |
| 15 | 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/ | 374 | 1 repo | ~8.5k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 16 | CLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments. | jaechang-hits/ | 374 | 1 repo | ~4.1k | Automated safety check: Pass | MIT | 12 days ago |
| 17 | 17.Pysam Genomic file toolkit. An agent skill from aipoch/medical-research-skills. | aipoch/ | 1.9k | — | ~3.4k | Automated safety check: Pass | MIT | 24 days ago |
| 18 | Read/write SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 1 repo | ~5.2k | Automated safety check: Pass | MIT | 12 days ago |
