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Research & Science · By FreedomIntelligence
Skills
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| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 1 | Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. | FreedomIntelligence/ | 3.1k | 2 repos | ~2k | Automated safety check: Pass | Apache-2.0 | 2 mo ago |
| 2 | FHIR API development guide for building healthcare endpoints. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.5k | Automated safety check: Pass | No licence | 2 mo ago |
| 3 | Query 14+ biomedical databases for drug repurposing, target discovery, clinical trials, and literature research. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.4k | Automated safety check: Pass | No licence | 2 mo ago |
| 4 | Parse, navigate, and query materials science ontology structure (classes, properties, hierarchy). | FreedomIntelligence/ | 3.1k | 1 repo | ~2k | Automated safety check: Notes | No licence | 2 mo ago |
| 5 | Map materials science terms, crystal structures, and sample descriptions to ontology classes and properties. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.9k | Automated safety check: Notes | No licence | 2 mo ago |
| 6 | Run bioinformatics analyses using Lobster AI - single-cell RNA-seq, bulk RNA-seq, literature mining, dataset discovery, quality control, and visualization. | FreedomIntelligence/ | 3.1k | 2 repos | ~2.5k | Automated safety check: Notes | No licence | 2 mo ago |
| 7 | 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 |
| 8 | Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation. | FreedomIntelligence/ | 3.1k | 2 repos | ~994 | Automated safety check: Pass | No licence | 2 mo ago |
| 9 | Process multiple sequence files in batch 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 |
| 10 | 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 |
| 11 | 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 |
| 12 | Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.2k | Automated safety check: Pass | No licence | 2 mo ago |
| 13 | Detects somatic mutations in circulating tumor DNA using variant callers optimized for low allele fractions with UMI-based error suppression. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.7k | Automated safety check: Pass | No licence | 2 mo ago |
| 14 | Perform differential expression analysis using DESeq2 in R/Bioconductor. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.8k | Automated safety check: Pass | No licence | 2 mo ago |
| 15 | Detect and track antimicrobial resistance genes using AMRFinderPlus and ResFinder with epidemiological context. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.9k | Automated safety check: Pass | No licence | 2 mo ago |
| 16 | Construct time-scaled phylogenies and infer evolutionary dynamics using TreeTime and BEAST2 for outbreak analysis. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.7k | Automated safety check: Pass | No licence | 2 mo ago |
| 17 | Infer pathogen transmission networks and identify likely transmission pairs using TransPhylo and outbreak reconstruction algorithms. | FreedomIntelligence/ | 3.1k | 1 repo | ~2k | Automated safety check: Pass | No licence | 2 mo ago |
| 18 | Assign pathogen lineages and track variants using Nextclade and pangolin for viral surveillance. | FreedomIntelligence/ | 3.1k | 1 repo | ~2k | Automated safety check: Pass | No licence | 2 mo ago |
| 19 | Filter and select sequences by criteria (length, ID, GC content, patterns) using Biopython. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.9k | Automated safety check: Pass | No licence | 2 mo ago |
| 20 | Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.5k | Automated safety check: Pass | No licence | 2 mo ago |
| 21 | 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 |
| 22 | Design guides for cytosine and adenine base editing using editing window optimization and BE-Hive outcome prediction. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.3k | Automated safety check: Pass | No licence | 2 mo ago |
| 23 | Design guide RNAs for CRISPR-Cas9/Cas12a experiments using CRISPRscan and local scoring algorithms. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.8k | Automated safety check: Pass | No licence | 2 mo ago |
| 24 | Design homology-directed repair donor templates for CRISPR knock-ins using primer3-py. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.2k | Automated safety check: Pass | No licence | 2 mo ago |
| 25 | Predict CRISPR off-target sites using Cas-OFFinder and CFD scoring algorithms. | FreedomIntelligence/ | 3.1k | 1 repo | ~2k | Automated safety check: Pass | No licence | 2 mo ago |
| 26 | Design pegRNAs for prime editing using PrimeDesign algorithms. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.4k | Automated safety check: Pass | No licence | 2 mo ago |
| 27 | Visualize Hi-C contact matrices, TADs, loops, and genomic features using matplotlib, cooltools, and HiCExplorer. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.2k | Automated safety check: Pass | No licence | 2 mo ago |
| 28 | Cell segmentation from multiplexed tissue images. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.7k | Automated safety check: Pass | No licence | 2 mo ago |
| 29 | 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 |
| 30 | Align long reads using minimap2 for Oxford Nanopore and PacBio data. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.3k | Automated safety check: Pass | No licence | 2 mo ago |
| 31 | Polish assemblies and call variants from Oxford Nanopore data using medaka. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.3k | Automated safety check: Pass | No licence | 2 mo ago |
| 32 | Species abundance estimation using Bracken with Kraken2 output. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.5k | Automated safety check: Pass | No licence | 2 mo ago |
| 33 | Detect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.8k | Automated safety check: Pass | No licence | 2 mo ago |
| 34 | Profile functional potential of metagenomes using HUMAnN3 and similar tools. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.9k | Automated safety check: Pass | No licence | 2 mo ago |
| 35 | Marker gene-based taxonomic profiling using MetaPhlAn 4. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.6k | Automated safety check: Pass | No licence | 2 mo ago |
| 36 | Track bacterial strains using MASH, sourmash, fastANI, and inStrain. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.9k | Automated safety check: Pass | No licence | 2 mo ago |
| 37 | Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.4k | Automated safety check: Pass | No licence | 2 mo ago |
| 38 | Preprocessing and harmonization of multi-omics data before integration. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.9k | Automated safety check: Pass | No licence | 2 mo ago |
| 39 | Multi-Omics Factor Analysis (MOFA2) for unsupervised integration of multiple data modalities. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.9k | Automated safety check: Pass | No licence | 2 mo ago |
| 40 | Handle paired-end FASTQ files (R1/R2) using Biopython. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.6k | Automated safety check: Pass | No licence | 2 mo ago |
| 41 | Perform geometric calculations on protein structures using Biopython Bio.PDB. | FreedomIntelligence/ | 3.1k | 1 repo | ~3.2k | Automated safety check: Pass | No licence | 2 mo ago |
| 42 | Parse and write protein structure files using Biopython Bio.PDB. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.9k | Automated safety check: Pass | No licence | 2 mo ago |
| 43 | Modify protein structures using Biopython Bio.PDB. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.8k | Automated safety check: Pass | No licence | 2 mo ago |
| 44 | Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.3k | Automated safety check: Pass | No licence | 2 mo ago |
| 45 | 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 |
| 46 | 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 |
| 47 | Peptide-spectrum matching and protein identification from MS/MS data. | FreedomIntelligence/ | 3.1k | 1 repo | ~983 | Automated safety check: Pass | No licence | 2 mo ago |
| 48 | Post-translational modification analysis including phosphorylation, acetylation, and ubiquitination. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.2k | Automated safety check: Pass | No licence | 2 mo ago |
