Results for “ancestrydna”

Query the Cancer Dependency Map (DepMap) for CRISPR gene dependency scores, drug sensitivity data, and gene effect profiles to identify cancer-specific vulnerabilities, synthetic lethal interactions, and validate oncology drug targets.

Query the Ensembl genome database REST API across 250+ species for gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, and Variant Effect Predictor (VEP) annotations. Use when mapping gene IDs or coordinates, fetching genomic sequence, finding orthologs across species, or predicting variant consequences for genomic research. Part of the AlterLab Academic Skills suite.

Build and analyze phylogenetic trees using MAFFT, IQ-TREE 2, and FastTree, with visualization via ETE3 or FigTree for evolutionary analysis, microbial genomics, viral phylodynamics, and molecular clock studies.

Reimplements DnaSP 6 for population genetics analysis of aligned DNA sequences, including nucleotide diversity, haplotype statistics, neutrality tests, linkage disequilibrium, recombination, mismatch distribution, InDel polymorphism, between-population divergence, outgroup-based tests, HKA test, McDonald-Kreitman.

Perform differential gene expression analysis for bulk RNA-seq data using PyDESeq2, supporting formulaic designs, Wald tests, FDR correction, LFC shrinkage, and result visualization.

Query the 1000 Genomes Project dataset at the individual participant level to find variants, carriers, and relatedness information.

Orchestrates a complete bulk RNA-seq differential-expression study from raw FASTQ reads through QC, alignment, quantification, differential expression, pathway enrichment, and publication figures.

Analyze any text to extract a cognitive fingerprint across 12 dimensions, revealing reasoning patterns, decision styles, and thinking signatures.

Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores, drug sensitivity data, and gene effect profiles to identify cancer-specific vulnerabilities, synthetic lethal interactions, and validate oncology drug targets.

Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifying cancer-specific vulnerabilities, synthetic lethal interactions, and validating oncology drug targets.

Calculate polygenic risk scores from direct-to-consumer genetic data using published scoring files from the PGS Catalog and contextualize results against population reference distributions.