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Research & Science · Python · By FreedomIntelligence
Skills
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| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 1 | Guide through omicverse's alignment module for SRA downloading, FASTQ quality control, STAR alignment, gene quantification, and single-cell kallisto/bustools pipelines covering both bulk and… | FreedomIntelligence/ | 3.1k | 2 repos | ~2k | Automated safety check: Pass | No licence | 2 mo ago |
| 2 | Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal using fgbio. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.6k | Automated safety check: Pass | No licence | 2 mo ago |
| 3 | Read and write compressed sequence files (gzip, bzip2, BGZF) using Biopython. | FreedomIntelligence/ | 3.1k | 1 repo | ~2k | Automated safety check: Pass | No licence | 2 mo ago |
| 4 | Analyzes cfDNA fragment size distributions and fragmentomics features using FinaleToolkit or Griffin. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.6k | Automated safety check: Pass | No licence | 2 mo ago |
| 5 | Predict B-cell and T-cell epitopes using BepiPred, IEDB tools, and structure-based methods for vaccine and antibody design. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.1k | Automated safety check: Pass | No licence | 2 mo ago |
| 6 | Load and parse mass spectrometry data formats including mzML, mzXML, and quantification tool outputs like MaxQuant proteinGroups.txt. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.2k | Automated safety check: Pass | No licence | 2 mo ago |
| 7 | Data-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.8k | Automated safety check: Pass | No licence | 2 mo ago |
| 8 | Protein quantification from mass spectrometry data including label-free (LFQ, intensity-based), isobaric labeling (TMT, iTRAQ), and metabolic labeling (SILAC) approaches. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.2k | Automated safety check: Pass | No licence | 2 mo ago |
| 9 | Infer cell-cell communication networks from scRNA-seq data using CellChat, NicheNet, and LIANA for ligand-receptor interaction analysis. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.2k | Automated safety check: Pass | No licence | 2 mo ago |
| 10 | Read, write, and create single-cell data objects using Seurat (R) and Scanpy (Python). | FreedomIntelligence/ | 3.1k | 1 repo | ~2k | Automated safety check: Pass | No licence | 2 mo ago |
| 11 | Detect and remove doublets (multiple cells captured in one droplet) from single-cell RNA-seq data. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.7k | Automated safety check: Pass | No licence | 2 mo ago |
| 12 | Quality control, filtering, and normalization for single-cell RNA-seq using Seurat (R) and Scanpy (Python). | FreedomIntelligence/ | 3.1k | 1 repo | ~2.4k | Automated safety check: Pass | No licence | 2 mo ago |
| 13 | Predict protein structures using modern ML models including AlphaFold3, ESMFold, Chai-1, and Boltz-1. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.5k | Automated safety check: Pass | No licence | 2 mo ago |
| 14 | Deep learning-based variant calling from long reads using Clair3 for SNPs and small indels. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.8k | Automated safety check: Pass | No licence | 2 mo ago |
| 15 | Integrate multiple scRNA-seq samples/batches using Harmony, scVI, Seurat anchors, and fastMNN. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.4k | Automated safety check: Pass | No licence | 2 mo ago |
| 16 | Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python). | FreedomIntelligence/ | 3.1k | 1 repo | ~2k | Automated safety check: Pass | No licence | 2 mo ago |
| 17 | Find marker genes and annotate cell types in single-cell RNA-seq using Seurat (R) and Scanpy (Python). | FreedomIntelligence/ | 3.1k | 1 repo | ~2.2k | Automated safety check: Pass | No licence | 2 mo ago |
| 18 | Analyze multi-modal single-cell data (CITE-seq, Multiome, spatial). | FreedomIntelligence/ | 3.1k | 1 repo | ~1.7k | Automated safety check: Pass | No licence | 2 mo ago |
| 19 | Statistical methods for calling hits in CRISPR screens. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. | FreedomIntelligence/ | 3.1k | — | ~2.3k | Automated safety check: Pass | No licence | 2 mo ago |
| 20 | Reads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel. | FreedomIntelligence/ | 3.1k | — | ~1.5k | Automated safety check: Pass | No licence | 2 mo ago |
| 21 | Analyzes alternative splicing at single-cell resolution using BRIE2 for probabilistic PSI estimation or leafcutter2 for cluster-based analysis with NMD detection. | FreedomIntelligence/ | 3.1k | — | ~1.6k | Automated safety check: Pass | No licence | 2 mo ago |
| 22 | Assesses RNA-seq data quality for splicing analysis including junction saturation curves, splice site strength scoring, and junction coverage metrics using RSeQC. | FreedomIntelligence/ | 3.1k | — | ~1.6k | Automated safety check: Pass | No licence | 2 mo ago |
| 23 | De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. | FreedomIntelligence/ | 3.1k | — | ~2.6k | Automated safety check: Pass | No licence | 2 mo ago |
| 24 | Query gnomAD for population allele frequencies to assess variant rarity. | FreedomIntelligence/ | 3.1k | — | ~1.7k | Automated safety check: Pass | No licence | 2 mo ago |
| 25 | Visualize copy number profiles, segments, and compare across samples. | FreedomIntelligence/ | 3.1k | — | ~2.6k | Automated safety check: Pass | No licence | 2 mo ago |
| 26 | JACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens) for modeling sgRNA efficacy and gene essentiality. | FreedomIntelligence/ | 3.1k | — | ~2.3k | Automated safety check: Pass | No licence | 2 mo ago |
| 27 | Statistical testing for differentially abundant proteins between conditions. | FreedomIntelligence/ | 3.1k | — | ~1.2k | Automated safety check: Pass | No licence | 2 mo ago |
