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Research & Science · By FreedomIntelligence
Skills
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| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 49 | 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 |
| 50 | Build, manage, and search spectral libraries for proteomics. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.8k | Automated safety check: Pass | No licence | 2 mo ago |
| 51 | Detect sample contamination and cross-species reads using FastQ Screen. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.6k | Automated safety check: Pass | No licence | 2 mo ago |
| 52 | Extract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umitools. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.4k | Automated safety check: Pass | No licence | 2 mo ago |
| 53 | Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) using Biopython Bio.SeqIO. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.6k | Automated safety check: Pass | No licence | 2 mo ago |
| 54 | 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 |
| 55 | 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 |
| 56 | 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 |
| 57 | Reconstruct cell lineage trees from CRISPR barcode tracing or mitochondrial mutations. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.1k | Automated safety check: Pass | No licence | 2 mo ago |
| 58 | Analyze metabolite-mediated cell-cell communication using MeboCost for metabolic signaling inference between cell types. | FreedomIntelligence/ | 3.1k | 1 repo | ~2k | Automated safety check: Pass | No licence | 2 mo ago |
| 59 | Analyze Perturb-seq and CROP-seq CRISPR screening data integrated with scRNA-seq. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.8k | Automated safety check: Pass | No licence | 2 mo ago |
| 60 | 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 |
| 61 | Single-cell ATAC-seq analysis with Signac (R/Seurat) and ArchR. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.6k | Automated safety check: Pass | No licence | 2 mo ago |
| 62 | Infer developmental trajectories and pseudotime from single-cell RNA-seq data using Monocle3, Slingshot, and scVelo for RNA velocity analysis. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.8k | Automated safety check: Pass | No licence | 2 mo ago |
| 63 | Process and analyze tissue images from spatial transcriptomics data using Squidpy. | FreedomIntelligence/ | 3.1k | 1 repo | ~2k | Automated safety check: Pass | No licence | 2 mo ago |
| 64 | Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData. | FreedomIntelligence/ | 3.1k | 1 repo | ~2k | Automated safety check: Pass | No licence | 2 mo ago |
| 65 | Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.6k | Automated safety check: Pass | No licence | 2 mo ago |
| 66 | Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalization. | FreedomIntelligence/ | 3.1k | 1 repo | ~976 | Automated safety check: Pass | No licence | 2 mo ago |
| 67 | Access and analyze AlphaFold protein structure predictions. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.1k | Automated safety check: Pass | No licence | 2 mo ago |
| 68 | 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 |
| 69 | Perform V(D)J alignment and clonotype assembly from TCR-seq or BCR-seq data using MiXCR. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.2k | Automated safety check: Pass | No licence | 2 mo ago |
| 70 | Estimates circulating tumor DNA fraction from shallow whole-genome sequencing using ichorCNA. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.6k | Automated safety check: Pass | No licence | 2 mo ago |
| 71 | Call SNPs and indels from aligned reads using bcftools mpileup and call. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.8k | Automated safety check: Pass | No licence | 2 mo ago |
| 72 | Clinical variant interpretation using ClinVar, ACMG guidelines, and pathogenicity predictors. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.8k | Automated safety check: Pass | No licence | 2 mo ago |
| 73 | Deep learning-based variant calling with Google DeepVariant. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.3k | Automated safety check: Pass | No licence | 2 mo ago |
| 74 | Comprehensive variant filtering including GATK VQSR, hard filters, bcftools expressions, and quality metric interpretation for SNPs and indels. | FreedomIntelligence/ | 3.1k | 1 repo | ~3.1k | Automated safety check: Pass | No licence | 2 mo ago |
| 75 | Joint genotype calling across multiple samples using GATK CombineGVCFs and GenotypeGVCFs. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.1k | Automated safety check: Pass | No licence | 2 mo ago |
| 76 | Search PubMed for scientific literature. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. | FreedomIntelligence/ | 3.1k | 1 repo | ~751 | Automated safety check: Pass | No licence | 2 mo ago |
| 77 | Perform differential expression analysis using edgeR in R/Bioconductor. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.9k | Automated safety check: Pass | No licence | 2 mo ago |
| 78 | Remove batch effects from RNA-seq data using ComBat, ComBat-Seq, limma removeBatchEffect, and SVA for unknown batch variables. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.1k | Automated safety check: Pass | No licence | 2 mo ago |
| 79 | Analyze time-series RNA-seq data using limma voom with splines, maSigPro, and ImpulseDE2. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.6k | Automated safety check: Pass | No licence | 2 mo ago |
| 80 | Perform multi-locus sequence typing (MLST), core genome MLST, and SNP-based strain typing for bacterial isolate characterization using mlst and chewBBACA. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.5k | Automated safety check: Pass | No licence | 2 mo ago |
| 81 | Work with FASTQ quality scores using Biopython. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.2k | Automated safety check: Pass | No licence | 2 mo ago |
| 82 | Variant calling with GATK HaplotypeCaller following best practices. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.8k | Automated safety check: Pass | No licence | 2 mo ago |
| 83 | Detect A/B compartments from Hi-C data using cooltools and eigenvector decomposition. | FreedomIntelligence/ | 3.1k | 1 repo | ~2k | Automated safety check: Pass | No licence | 2 mo ago |
| 84 | Cell type assignment from marker expression in IMC data. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.7k | Automated safety check: Pass | No licence | 2 mo ago |
| 85 | Identify tumor neoantigens from somatic mutations using pVACtools for personalized cancer immunotherapy. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.4k | Automated safety check: Pass | No licence | 2 mo ago |
| 86 | 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 |
| 87 | Taxonomic classification of metagenomic reads using Kraken2. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.5k | Automated safety check: Pass | No licence | 2 mo ago |
| 88 | Extract methylation calls from Bismark BAM files using bismarkmethylationextractor. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.5k | Automated safety check: Pass | No licence | 2 mo ago |
| 89 | Differentially methylated region (DMR) detection using methylKit tiles, bsseq BSmooth, and DMRcate. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.5k | Automated safety check: Pass | No licence | 2 mo ago |
| 90 | DNA methylation analysis with methylKit in R. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.5k | Automated safety check: Pass | No licence | 2 mo ago |
| 91 | Alpha and beta diversity analysis for microbiome data. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.4k | Automated safety check: Pass | No licence | 2 mo ago |
| 92 | Predict metagenome functional content from 16S rRNA marker gene data using PICRUSt2. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.2k | Automated safety check: Pass | No licence | 2 mo ago |
| 93 | Similarity Network Fusion (SNF) for patient stratification using multi-omics data. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.9k | Automated safety check: Pass | No licence | 2 mo ago |
| 94 | KEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and enrichMKEGG. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.7k | Automated safety check: Pass | No licence | 2 mo ago |
| 95 | Reactome pathway enrichment using ReactomePA package. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.6k | Automated safety check: Pass | No licence | 2 mo ago |
| 96 | Protein grouping and inference from peptide identifications. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.4k | Automated safety check: Pass | No licence | 2 mo ago |
