Results for “rna”

Analyze single-cell RNA-seq data with Scanpy, covering quality control, normalization, dimensionality reduction, clustering, marker gene identification, and visualization.

Analyze single-cell RNA-seq data with Scanpy, covering quality control, normalization, clustering, marker gene identification, visualization, and trajectory analysis.

Run standard single-cell RNA-seq analysis pipelines: QC, normalization, dimensionality reduction, clustering, differential expression, and visualization using Scanpy.

Analyze single-cell RNA-seq data with Scanpy, covering quality control, normalization, clustering, marker gene identification, visualization, and trajectory analysis.

Analyze single-cell RNA-seq data with Scanpy, covering quality control, normalization, clustering, marker gene identification, visualization, and trajectory analysis.

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

Process and analyze high-throughput sequencing data with deepTools for quality control, normalization, comparison, and publication-quality visualizations of ChIP-seq, RNA-seq, and ATAC-seq experiments.

Infer gene regulatory networks from gene expression data using scalable algorithms (GRNBoost2, GENIE3) with support for distributed computation.

Index local folders and search documents with BM25, vector, or hybrid queries, plus AI answers with citations and a web UI.

Performs deep root cause analysis on NVIDIA TAO Visual ChangeNet classification experiments, using image-evidence-driven investigation to diagnose model failures and produce actionable reports.

Evaluates RAG pipelines using a filesystem-based benchmark with corpus/ and train.json, running evaluate_rag.py to tune retrieval and generation flags and interpret RAGAS metrics.

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.

Integrate with Benchling's Python SDK and REST API to manage registry entities, inventory, ELN entries, workflows, and Data Warehouse queries for life sciences R&D automation.

Provides deep generative models for single-cell omics analysis, including probabilistic batch correction, transfer learning, differential expression, and multi-modal integration.

Analyze biological sequences, alignments, phylogenetic trees, and diversity metrics (alpha/beta, UniFrac) with ordination (PCoA) and PERMANOVA for microbiome and community ecology data.

Annotates single-cell RNA-seq data by scoring marker genes, transferring labels with CellTypist, or reasoning over cluster markers with an LLM.

Runs standard single-cell RNA-seq analysis with Scanpy, covering QC, normalization, dimensionality reduction, clustering, marker identification, visualization, and conversion of R single-cell formats to h5ad.

Access NCBI GEO (Gene Expression Omnibus) for gene expression and functional genomics data — search and download microarray and RNA-seq datasets by GSE, GSM, GPL, or GDS accession and retrieve SOFT, MINiML, and series matrix files. Use when locating public expression datasets, fetching processed expression matrices, downloading a study's supplementary files, or sourcing per-study transcriptomics data for differential-expression analysis. For raw FASTQ sequencing reads by SRA/ENA run accession use alterlab-ena; for reference tissue-expression baselines (median TPM across human tissues) use alterlab-gtex; for cancer cohort somatic mutations and copy-number use alterlab-cbioportal. Part of the AlterLab Academic Skills suite.

Query cBioPortal via its keyless REST API for cancer genomics across TCGA, GENIE, MSK-IMPACT and hundreds of studies — somatic mutations, copy-number alterations (GISTIC), mRNA/protein expression, structural variants, and patient-level clinical/survival data. Use when asked how often a gene is mutated/amplified/deleted in a tumor type, to profile oncogenes or tumor suppressors across cancers (pan-cancer alteration frequency), to pull patient-level mutations joined to OS/clinical outcomes, or to validate a cancer target from cohort genomics. For germline variant pathogenicity use alterlab-clinvar; for mutational-signature (SBS) decomposition use alterlab-cosmic; for CRISPR/RNAi gene-dependency use alterlab-depmap; for aggregated target-disease evidence use alterlab-opentargets. Part of the AlterLab Academic Skills suite.