Topic · Research & Science
Best bioinformatics skills, page 8
Bioinformatics skills, ranked
Ranked by score. Sort bymost stars,trending,newest,recently updated
| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 337 | 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 |
| 338 | 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 |
| 339 | 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 |
| 340 | 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 |
| 341 | 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 |
| 342 | 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 |
| 343 | 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 |
| 344 | Build, manage, and search spectral libraries for proteomics. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.8k | Automated safety check: Pass | No licence | 2 mo ago |
| 345 | 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 |
| 346 | 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 |
| 347 | 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 |
| 348 | 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 |
| 349 | 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 |
| 350 | 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 |
| 351 | 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 |
| 352 | 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 |
| 353 | 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 |
| 354 | 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 |
| 355 | 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 |
| 356 | 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 |
| 357 | 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 |
| 358 | 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 |
| 359 | 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 |
| 360 | 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 |
| 361 | 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 |
| 362 | 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 |
| 363 | 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 |
| 364 | 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 |
| 365 | Deep learning-based variant calling with Google DeepVariant. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.3k | Automated safety check: Pass | No licence | 2 mo ago |
| 366 | 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 |
| 367 | 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 |
| 368 | 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 |
| 369 | 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 |
| 370 | 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 |
| 371 | 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 |
| 372 | 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 |
| 373 | Variant calling with GATK HaplotypeCaller following best practices. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.8k | Automated safety check: Pass | No licence | 2 mo ago |
| 374 | 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 |
| 375 | 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 |
| 376 | 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 |
| 377 | Taxonomic classification of metagenomic reads using Kraken2. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.5k | Automated safety check: Pass | No licence | 2 mo ago |
| 378 | 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 |
| 379 | 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 |
| 380 | 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 |
| 381 | 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 |
| 382 | Protein grouping and inference from peptide identifications. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.4k | Automated safety check: Pass | No licence | 2 mo ago |
| 383 | Quality control and assessment for proteomics data. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.8k | Automated safety check: Pass | No licence | 2 mo ago |
| 384 | 384.Bio Rnaseq Qc RNA-seq specific quality control including rRNA contamination detection, strandedness verification, gene body coverage, and transcript integrity metrics. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.1k | Automated safety check: Pass | No licence | 2 mo ago |
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