Marker gene-based taxonomic profiling using MetaPhlAn 4. Provides accurate species-level relative abundances using clade-specific markers.
Marker gene-based taxonomic profiling using MetaPhlAn 4. Provides accurate species-level relative abundances using clade-specific markers.
Analyzes cfDNA methylation patterns for cancer detection using cfMeDIP-seq or bisulfite sequencing with MethylDackel.
Analyzes cfDNA methylation patterns for cancer detection using cfMeDIP-seq or bisulfite sequencing with MethylDackel.
Extract methylation calls from Bismark BAM files using bismark_methylation_extractor. Generates per-cytosine reports for CpG, CHG, and CHH contexts.
Extract methylation calls from Bismark BAM files using bismark_methylation_extractor. Generates per-cytosine reports for CpG, CHG, and CHH contexts.
Amplicon sequence variant (ASV) inference from 16S rRNA or ITS amplicon sequencing using DADA2. Covers quality filtering, error learning, denoising, and chimera removal — from…
Amplicon sequence variant (ASV) inference from 16S rRNA or ITS amplicon sequencing using DADA2. Covers quality filtering, error learning, denoising, and chimera removal — from…
QIIME2 command-line workflow for 16S/ITS amplicon analysis. Alternative to DADA2/phyloseq R workflow with built-in provenance tracking.
QIIME2 command-line workflow for 16S/ITS amplicon analysis. Alternative to DADA2/phyloseq R workflow with built-in provenance tracking.
Taxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (DADA2, IDTAXA) and exact matching approaches.
Taxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (DADA2, IDTAXA) and exact matching approaches.
Preprocessing and harmonization of multi-omics data before integration. Covers normalization, batch correction, feature alignment, and missing value handling across data — from…
Preprocessing and harmonization of multi-omics data before integration. Covers normalization, batch correction, feature alignment, and missing value handling across data — from…
Supervised and unsupervised multi-omics integration with mixOmics. Includes sPLS for pairwise integration and DIABLO for multi-block discriminant analysis.
Supervised and unsupervised multi-omics integration with mixOmics. Includes sPLS for pairwise integration and DIABLO for multi-block discriminant analysis.
Multi-Omics Factor Analysis (MOFA2) for unsupervised integration of multiple data modalities. Identifies shared and view-specific sources of variation.
Multi-Omics Factor Analysis (MOFA2) for unsupervised integration of multiple data modalities. Identifies shared and view-specific sources of variation.
Similarity Network Fusion (SNF) for patient stratification using multi-omics data. Integrates multiple data types into a unified patient similarity network.
Similarity Network Fusion (SNF) for patient stratification using multi-omics data. Integrates multiple data types into a unified patient similarity network.
Profile and bio optimization across X, Instagram, and note — craft compelling bios with USP, social proof, CTA, and keywords. The bio is where 80% of follow decisions happen.
Pull pre-computed ortholog calls from public databases (OrthoDB, Ensembl Compara, OMA browser, eggNOG, PANTHER, KEGG Orthology, HomoloGene) via their REST APIs.
Visualize enrichment results using enrichplot package functions. Use when creating publication-quality figures from clusterProfiler results.
Visualize enrichment results using enrichplot package functions. Use when creating publication-quality figures from clusterProfiler results.
Gene Set Enrichment Analysis using clusterProfiler gseGO and gseKEGG. Use when analyzing ranked gene lists to find coordinated expression changes in gene sets without arb — from…
Gene Set Enrichment Analysis using clusterProfiler gseGO and gseKEGG. Use when analyzing ranked gene lists to find coordinated expression changes in gene sets without arb — from…
KEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and enrichMKEGG. Use when identifying metabolic and signaling pathways over-represented in a — from…
KEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and enrichMKEGG. Use when identifying metabolic and signaling pathways over-represented in a — from…
Reactome pathway enrichment using ReactomePA package. Use when analyzing gene lists against Reactome's curated peer-reviewed pathway database.
Reactome pathway enrichment using ReactomePA package. Use when analyzing gene lists against Reactome's curated peer-reviewed pathway database.
WikiPathways enrichment using clusterProfiler and rWikiPathways. Use when analyzing gene lists against community-curated open-source pathways.
WikiPathways enrichment using clusterProfiler and rWikiPathways. Use when analyzing gene lists against community-curated open-source pathways.
Impute missing genotypes using reference panels with Beagle or Minimac4. Use when increasing variant density for GWAS, harmonizing data across genotyping platforms, or in — from…
Phase genotypes into haplotypes using Beagle or SHAPEIT. Resolves which alleles are inherited together on each chromosome.
Quality control of phasing and imputation results. Filter by INFO scores, assess accuracy, and prepare imputed data for downstream analysis.
Run Bayesian phylogenetic analysis with MrBayes, BEAST2, RevBayes, and PhyloBayes including MCMC convergence diagnostics and model comparison.
Estimate species trees using coalescent methods including ASTRAL-III, wASTRAL, ASTRAL-Pro, SVDQuartets, and BPP.
Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating a — from…
PLINK file formats, format conversion, and quality control filtering for population genetics. Convert between VCF, BED/BIM/FAM, and PED/MAP formats, apply MAF, genotyping — from…
Analyze population structure using PCA and admixture analysis with PLINK and ADMIXTURE. Identify population clusters, assess ancestry proportions, visualize genetic struc — from…
Validates docked / generated protein-ligand poses using PoseBusters physical-validity tests, strain energy quantification, geometric checks (planarity, vdW overlap, bond/angle…
Design PCR primers for a target sequence using primer3-py. Specify target regions, product size, melting temperature, and other constraints.
Load and parse mass spectrometry data formats including mzML, mzXML, and quantification tool outputs like MaxQuant proteinGroups.txt.
Load and parse mass spectrometry data formats including mzML, mzXML, and quantification tool outputs like MaxQuant proteinGroups.txt.
Data-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Use when analyzing DIA mass spectrometry data with library-free or library-based workf — from…
Data-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Use when analyzing DIA mass spectrometry data with library-free or library-based workf — from…
Protein grouping and inference from peptide identifications. Use when resolving protein ambiguity from shared peptides.
Protein grouping and inference from peptide identifications. Use when resolving protein ambiguity from shared peptides.
Quality control and assessment for proteomics data. Use when evaluating proteomics data quality before downstream analysis.
Quality control and assessment for proteomics data. Use when evaluating proteomics data quality before downstream analysis.
Protein quantification from mass spectrometry data including label-free (LFQ, intensity-based), isobaric labeling (TMT, iTRAQ), and metabolic labeling (SILAC) approaches — from…
Protein quantification from mass spectrometry data including label-free (LFQ, intensity-based), isobaric labeling (TMT, iTRAQ), and metabolic labeling (SILAC) approaches — from…
Build, manage, and search spectral libraries for proteomics. Use when creating or working with spectral libraries for DIA analysis.
Build, manage, and search spectral libraries for proteomics. Use when creating or working with spectral libraries for DIA analysis.
Enumerates chemical libraries through reaction SMARTS transformations using RDKit. Generates virtual compound libraries from building blocks using defined chemical reactions with…
Align short reads using Bowtie2 with local or end-to-end modes. Supports gapped alignment. Use when aligning ChIP-seq, ATAC-seq, or when flexible alignment modes are need — from…
Align RNA-seq reads with HISAT2, a memory-efficient splice-aware aligner. Use when STAR's memory requirements are too high or for general RNA-seq alignment.
Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Illumina TruSeq, Nextera, and custom adapter sequenc — from…
Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Illumina TruSeq, Nextera, and custom adapter sequenc — from…
All-in-one read preprocessing with fastp including adapter trimming, quality filtering, deduplication, base correction, and HTML report generation.