FreedomIntelligence
Showing 121–161 of 161 skills · Page 3 of 3
FreedomIntelligence / bio-clinical-databases-tumor-mutational-burden
3.0kCalculate tumor mutational burden from panel or WES data with proper normalization and clinical thresholds
FreedomIntelligence / bio-clinical-databases-variant-prioritization
3.0kFilter and prioritize variants by pathogenicity, population frequency, and clinical evidence for rare disease analysis
FreedomIntelligence / bio-clip-seq-clip-peak-calling
3.0kPureCLIP uses an HMM to model crosslink sites, incorporating enrichment and truncation signals.
FreedomIntelligence / bio-codon-usage
3.0kAnalyze codon usage patterns and calculate codon adaptation metrics using Biopython.
FreedomIntelligence / bio-compressed-files
3.0kRead and write compressed sequence files (gzip, bzip2, BGZF) using Biopython
FreedomIntelligence / bio-consensus-sequences
3.0kGenerate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus
FreedomIntelligence / bio-copy-number-cnv-annotation
3.0kAnnotate CNVs with genes, pathways, and clinical significance
FreedomIntelligence / bio-crispr-screens-base-editing-analysis
3.0kAnalyzes base editing and prime editing outcomes including editing efficiency, bystander edits, and indel frequencies
FreedomIntelligence / bio-crispr-screens-jacks-analysis
3.0kJACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens) for modeling sgRNA efficacy and gene essentiality
FreedomIntelligence / bio-data-visualization-circos-plots
3.0kCircular genome visualizations for displaying multiple data tracks around chromosome ideograms.
FreedomIntelligence / bio-entrez-fetch
3.0kRetrieve records from NCBI databases using Biopython's Entrez module (EFetch, ESummary utilities).
FreedomIntelligence / bio-entrez-link
3.0kNavigate between NCBI databases using Biopython's Entrez module (ELink utility).
FreedomIntelligence / bio-entrez-search
3.0kSearch NCBI databases using Biopython's Entrez module (ESearch, EInfo, EGQuery utilities).
FreedomIntelligence / bio-experimental-design-batch-design
3.0kBatch effects are unavoidable. Good design makes them correctable.
FreedomIntelligence / bio-experimental-design-multiple-testing
3.0kTesting 20,000 genes at p < 0.05 yields ~1,000 false positives by chance. Correction is essential.
FreedomIntelligence / bio-filter-sequences
3.0kFilter and select sequences by criteria (length, ID, GC content, patterns) using Biopython
FreedomIntelligence / bio-format-conversion
3.0kConvert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO
FreedomIntelligence / bio-genome-assembly-assembly-polishing
3.0kImprove assembly accuracy by correcting errors using additional sequencing data.
FreedomIntelligence / bio-genome-assembly-assembly-qc
3.0kEvaluate genome assembly quality with contiguity metrics (QUAST) and gene completeness (BUSCO).
FreedomIntelligence / bio-genome-assembly-long-read-assembly
3.0kAssemble genomes from Oxford Nanopore (ONT) or PacBio long reads for highly contiguous assemblies.
FreedomIntelligence / bio-genome-assembly-short-read-assembly
3.0kAssemble genomes from Illumina paired-end or single-end reads using SPAdes.
FreedomIntelligence / bio-genome-intervals-bed-file-basics
3.0kBED (Browser Extensible Data) format stores genomic intervals. Uses 0-based, half-open coordinates.
FreedomIntelligence / bio-genome-intervals-bigwig-tracks
3.0kBigWig is an indexed binary format for continuous genomic data. Efficient for genome browsers and programmatic access.
FreedomIntelligence / bio-genome-intervals-coverage-analysis
3.0kCalculate coverage and depth across genomic regions using bedtools and pybedtools.
FreedomIntelligence / bio-genome-intervals-gtf-gff-handling
3.0kGTF and GFF3 are standard gene annotation formats. Both use 1-based coordinates.
FreedomIntelligence / bio-genome-intervals-interval-arithmetic
3.0kCore set operations on genomic intervals using bedtools (CLI) and pybedtools (Python).
FreedomIntelligence / bio-genome-intervals-proximity-operations
3.0kOperations for finding nearby features and extending intervals using bedtools and pybedtools.
FreedomIntelligence / bio-geo-data
3.0kQuery and access Gene Expression Omnibus datasets using Biopython's Entrez module.
FreedomIntelligence / bio-imaging-mass-cytometry-quality-metrics
3.0kQuality metrics for IMC data including signal-to-noise, channel correlation, tissue integrity, and acquisition QC
FreedomIntelligence / bio-liquid-biopsy-pipeline
3.0kComplete workflow for cfDNA analysis from sequencing to clinical interpretation.
FreedomIntelligence / bio-local-blast
3.0kRun BLAST searches locally using NCBI BLAST+ command-line tools.
FreedomIntelligence / bio-long-read-sequencing-clair3-variants
3.0kDeep learning-based variant calling from long reads using Clair3 for SNPs and small indels
FreedomIntelligence / bio-long-read-sequencing-isoseq-analysis
3.0kAnalyze PacBio Iso-Seq data for full-length isoform discovery and quantification
FreedomIntelligence / bio-long-read-sequencing-nanopore-methylation
3.0kCalls DNA methylation from Oxford Nanopore sequencing data using signal-level analysis
FreedomIntelligence / bio-longread-structural-variants
3.0kDetect structural variants from long-read alignments using Sniffles, cuteSV, and SVIM
FreedomIntelligence / bio-machine-learning-biomarker-discovery
3.0kIdentifies all features that are significantly better than random (shadow features).
FreedomIntelligence / bio-alignment-files-bam-statistics
3.0kGenerate alignment statistics using samtools and pysam.
FreedomIntelligence / bio-batch-processing
3.0kProcess multiple sequence files in batch using Biopython
FreedomIntelligence / bio-duplicate-handling
3.0kMark and remove PCR/optical duplicates using samtools.
FreedomIntelligence / bio-epitranscriptomics-m6anet-analysis
3.0kDocumentation: https://m6anet.readthedocs.io/
FreedomIntelligence / bio-fastq-quality
3.0kWork with FASTQ quality scores using Biopython