1,133 skills found · Page 18 of 38
FreedomIntelligence / benchling-integrationBenchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
FreedomIntelligence / bio-alignment-msa-statisticsCalculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics
FreedomIntelligence / bio-crispr-screens-library-designCRISPR library design for genetic screens. Covers sgRNA selection, library composition, control design, and oligo ordering
FreedomIntelligence / anndataThis skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling large-scale biological datasets
FreedomIntelligence / bio-admet-predictionPredicts ADMET properties using ADMETlab 3.0 API or DeepChem models. Estimates bioavailability, CYP inhibition, hERG liability, and 119 toxicity endpoints with uncertainty quantification. Filters for PAINS and other structural alerts
FreedomIntelligence / bio-alignment-ioRead, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis
FreedomIntelligence / bio-alignment-msa-parsingParse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis
FreedomIntelligence / bio-atac-seq-atac-qcQuality control metrics for ATAC-seq data including fragment size distribution, TSS enrichment, FRiP, and library complexity
FreedomIntelligence / bio-chipseq-motif-analysisDe novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor binding motifs in ChIP-seq, ATAC-seq, or other genomic peak data
FreedomIntelligence / bio-clinical-databases-somatic-signaturesExtract and analyze mutational signatures from somatic variants using SigProfiler or MutationalPatterns to characterize mutagenic processes
FreedomIntelligence / bio-copy-number-cnv-visualizationVisualize copy number profiles, segments, and compare across samples. Create publication-quality plots of CNV data from CNVkit, GATK, or other callers
FreedomIntelligence / bio-copy-number-cnvkit-analysisDetect copy number variants from targeted/exome sequencing using CNVkit. Supports tumor-normal pairs, tumor-only, and germline CNV calling
FreedomIntelligence / bio-crispr-screens-batch-correctionBatch effect correction for CRISPR screens. Covers normalization across batches, technical replicate handling, and batch-aware analysis
FreedomIntelligence / bio-crispr-screens-crispresso-editingCRISPResso2 for analyzing CRISPR gene editing outcomes. Quantifies indels, HDR efficiency, and generates comprehensive editing reports
FreedomIntelligence / bio-crispr-screens-hit-callingStatistical methods for calling hits in CRISPR screens. Covers MAGeCK, BAGEL2, drugZ, and custom approaches for identifying essential and resistance genes
FreedomIntelligence / bio-crispr-screens-mageck-analysisMAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) for pooled CRISPR screen analysis. Covers count normalization, gene ranking, and pathway analysis
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-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-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-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
