12,425 skills found · Page 184 of 415
FreedomIntelligence / bio-crispr-screens-screen-qcQuality control for pooled CRISPR screens. Covers library representation, read distribution, replicate correlation, and essential gene recovery
FreedomIntelligence / bio-ctdna-mutation-detectionDetects somatic mutations in circulating tumor DNA using variant callers optimized for low allele fractions with UMI-based error suppression. Reliably detects mutations at VAF above 0.5 percent using consensus-based approaches
FreedomIntelligence / bio-data-visualization-specialized-omics-plotsThis skill provides reusable plotting functions for common omics visualizations that can be applied across different analysis types: - Volcano plots (any DE result) - MA plots (any log-fold-change data) - PCA plots (any high-dimensional data) - Enrichment dotplots (manual, not enrichplot) - Expressi…
FreedomIntelligence / bio-de-deseq2-basicsPerform differential expression analysis using DESeq2 in R/Bioconductor. Use for analyzing RNA-seq count data, creating DESeqDataSet objects, running the DESeq workflow, and extracting results with log fold change shrinkage
FreedomIntelligence / bio-de-edger-basicsPerform differential expression analysis using edgeR in R/Bioconductor. Use for analyzing RNA-seq count data with the quasi-likelihood F-test framework, creating DGEList objects, normalization, dispersion estimation, and statistical testing
FreedomIntelligence / bio-de-resultsExtract, filter, annotate, and export differential expression results from DESeq2 or edgeR. Use for identifying significant genes, applying multiple testing corrections, adding gene annotations, and preparing results for downstream analysis
FreedomIntelligence / bio-differential-expression-batch-correctionRemove batch effects from RNA-seq data using ComBat, ComBat-Seq, limma removeBatchEffect, and SVA for unknown batch variables
FreedomIntelligence / bio-differential-expression-timeseries-deAnalyze time-series RNA-seq data using limma voom with splines, maSigPro, and ImpulseDE2. Identify genes with dynamic expression patterns
FreedomIntelligence / bio-differential-splicingDetects differential alternative splicing between conditions using rMATS-turbo (BAM-based) or SUPPA2 diffSplice (TPM-based). Reports events with FDR-corrected significance and delta PSI effect sizes
FreedomIntelligence / bio-epidemiological-genomics-amr-surveillanceDetect and track antimicrobial resistance genes using AMRFinderPlus and ResFinder with epidemiological context. Monitor resistance trends and identify emerging resistance patterns
FreedomIntelligence / bio-epidemiological-genomics-pathogen-typingPerform multi-locus sequence typing (MLST), core genome MLST, and SNP-based strain typing for bacterial isolate characterization using mlst and chewBBACA
FreedomIntelligence / bio-epidemiological-genomics-phylodynamicsConstruct time-scaled phylogenies and infer evolutionary dynamics using TreeTime and BEAST2 for outbreak analysis. Estimate divergence times, molecular clock rates, and ancestral states
FreedomIntelligence / bio-epidemiological-genomics-transmission-inferenceInfer pathogen transmission networks and identify likely transmission pairs using TransPhylo and outbreak reconstruction algorithms. Estimate who-infected-whom from genomic and epidemiological data
FreedomIntelligence / bio-epidemiological-genomics-variant-surveillanceAssign pathogen lineages and track variants using Nextclade and pangolin for viral surveillance. Monitor variant prevalence and identify emerging variants of concern
FreedomIntelligence / bio-flow-cytometry-bead-normalizationBead-based normalization for CyTOF and high-parameter flow cytometry. Covers EQ bead normalization, signal drift correction, and batch normalization
FreedomIntelligence / bio-flow-cytometry-clustering-phenotypingUnsupervised clustering and cell type identification for flow/mass cytometry. Covers FlowSOM, Phenograph, and CATALYST workflows
FreedomIntelligence / bio-flow-cytometry-cytometry-qcComprehensive quality control for flow cytometry and CyTOF data. Covers flow rate stability, signal drift, margin events, dead cell exclusion, and batch QC
FreedomIntelligence / bio-flow-cytometry-doublet-detectionDetect and remove doublets from flow and mass cytometry data. Covers FSC/SSC gating and computational doublet detection methods
FreedomIntelligence / bio-fragment-analysisAnalyzes cfDNA fragment size distributions and fragmentomics features using FinaleToolkit or Griffin. Extracts nucleosome positioning patterns, fragment ratios, and DELFI-style fragmentation profiles for cancer detection
FreedomIntelligence / bio-gatk-variant-callingVariant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint genotyping, and variant quality score recalibration (VQSR)
FreedomIntelligence / bio-genome-assembly-metagenome-assemblyMetagenome assembly reconstructs genomes from mixed microbial communities. Long reads enable recovery of complete circular genomes and resolution of strain-level differences.
FreedomIntelligence / bio-genome-engineering-base-editing-designDesign guides for cytosine and adenine base editing using editing window optimization and BE-Hive outcome prediction. Select optimal positions for C-to-T or A-to-G conversions without double-strand breaks
FreedomIntelligence / bio-genome-engineering-grna-designDesign guide RNAs for CRISPR-Cas9/Cas12a experiments using CRISPRscan and local scoring algorithms. Score guides for on-target activity using Rule Set 2 and Azimuth models
FreedomIntelligence / bio-genome-engineering-hdr-template-designDesign homology-directed repair donor templates for CRISPR knock-ins using primer3-py. Create ssODN, dsDNA, or plasmid templates with optimized homology arms
FreedomIntelligence / bio-genome-engineering-off-target-predictionPredict CRISPR off-target sites using Cas-OFFinder and CFD scoring algorithms. Identify potential unintended cleavage sites genome-wide and assess guide specificity
FreedomIntelligence / bio-genome-engineering-prime-editing-designDesign pegRNAs for prime editing using PrimeDesign algorithms. Generate spacer, PBS, and RT template sequences for precise genomic modifications without double-strand breaks
FreedomIntelligence / bio-hi-c-analysis-compartment-analysisDetect A/B compartments from Hi-C data using cooltools and eigenvector decomposition. Identify active (A) and inactive (B) chromatin compartments from contact matrices
FreedomIntelligence / bio-hi-c-analysis-contact-pairsProcess Hi-C read pairs using pairtools. Parse alignments, filter duplicates, classify pairs, and generate contact statistics from Hi-C sequencing data
FreedomIntelligence / bio-hi-c-analysis-hic-data-ioLoad, convert, and manipulate Hi-C contact matrices using cooler format. Read .cool/.mcool files, convert from .hic format, access matrix data, and export to different formats
FreedomIntelligence / bio-hi-c-analysis-hic-differentialCompare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold changes, statistical significance, and visualize differential contact maps
