ACE

bwa-meth -- fast and accurate bisulfite-seq (WGBS/RRBS) aligner built on BWA-MEM. Performs in-silico C-to-T conversion of reads and reference, aligns with BWA-MEM or BWA-MEM2, and recovers original ba

1 shared topic • 2 shared operations

Cellranger-arc — 10x Genomics pipeline for processing Multiome ATAC + Gene Expression data from the Chromium Multiome kit. Aligns FASTQ reads, calls peaks, quantifies gene expression and chromatin acc

1 shared topic • 2 shared operations

FLAMES — Full-Length Analysis of Mutations and Splicing for bulk and single-cell long-read RNA-seq data. R/Bioconductor pipeline for barcode demultiplexing, isoform discovery, transcript quantificatio

1 shared topic • 2 shared operations

Use when performing single-cell QTL (sc-eQTL, sc-sQTL) mapping with SAIGE-QTL. SAIGE-QTL extends the SAIGE framework to single-cell RNA-seq data using Poisson mixed models to handle count overdispersi

1 shared topic • 2 shared operations

salmon — Fast, bias-aware transcript quantification from RNA-seq data using selective alignment to the transcriptome. Supports bulk RNA-seq (mapping-based and alignment-based modes), single-cell RNA-s

1 shared topic • 2 shared operations