Dr. Alex M. Mawla, PhD
Community@ammawla · Sacramento, CA
Computational geneticist
Agent Skills by Dr. Alex M. Mawla, PhD
Showing 48 vetted skills indexed across 1 GitHub repositories.
ammawlafunctional-screen-analysis
Analyze ENCODE CRISPR, MPRA, and STARR-seq screens to validate regulatory elements.
ammawlacite-encode
Generate BibTeX and RIS citations for ENCODE datasets and publications.
ammawlavariant-annotation
Analyze genetic variant overlaps with ENCODE regulatory elements and clinical data.
ammawlascrna-meta-analysis
Integrate and validate single-cell RNA-seq datasets across studies.
ammawlapipeline-wgbs
Process WGBS FASTQ files into ENCODE-compliant methylation calls.
ammawlahic-aggregation
Aggregate Hi-C loop calls from multiple experiments into a union chromatin contact catalog.
ammawlasingle-cell-encode
Discover, retrieve, and integrate ENCODE single-cell datasets across tissues and assays.
ammawlagtex-expression
Retrieve GTEx median TPM values to validate ENCODE regulatory findings.
ammawlaquality-assessment
Analyze ENCODE experimental data quality using audit flags and QC metrics.
ammawlaucsc-browser
Access UCSC genome annotations, sequences, and track data via REST API.
ammawlapipeline-guide
Guide selection, configuration, and execution of ENCODE genomics pipelines across compute environments.
ammawlaepigenome-profiling
Integrate ENCODE histone modification, accessibility, methylation, and 3D conformation data with ChromHMM chromatin state modeling.
ammawlaliftover-coordinates
Convert genomic coordinates between genome assemblies with provenance tracking.
ammawlatrack-experiments
Track ENCODE experiment metadata, citations, and provenance locally.
ammawlapipeline-atacseq
Automate ATAC-seq processing and peak calling from raw FASTQ reads.
ammawlaclinvar-annotation
Map ClinVar variants to ENCODE regulatory regions for disease association.
ammawlabatch-analysis
Identify, QC-filter, and organize ENCODE experiment collections for batch downloads.
ammawlapipeline-chipseq
Automate ChIP-seq analysis from raw reads to peak calling with ENCODE guidelines.
ammawlasetup
Guide installation, configuration, and troubleshooting of the ENCODE Toolkit server.
ammawlapeak-annotation
Annotate ENCODE ChIP-seq and ATAC-seq peaks with genomic features.
ammawlaregulatory-elements
Classify genomic regulatory elements from ENCODE chromatin signatures.
ammawlacellxgene-context
Identifies cell types underlying ENCODE signals via single-cell expression profiles.
ammawlascientific-writing
Generate methods sections and figure legends from ENCODE provenance metadata.
ammawlapublication-trust
Assess publication trust by checking retractions, corrections, and contradiction evidence.