SortMeRNA

DecontX — R/Bioconductor method in the celda package for estimating and removing ambient RNA contamination from droplet-based single-cell RNA-seq data. Uses a Bayesian Dirichlet mixture model over cel

2 shared topics • 2 shared operations

FLAIR — Full-Length Alternative Isoform analysis of RNA for long-read sequencing. Corrects, defines, and quantifies transcript isoforms from nanopore cDNA, native RNA, and PacBio reads. Provides splic

2 shared topics • 2 shared operations

Qualimap — platform-independent quality control tool for next-generation sequencing alignment data. Provides BAM QC (coverage, insert size, GC content, mapping quality), RNA-seq QC (gene body coverage

2 shared topics • 2 shared operations

Rcorrector — kmer-based error correction for RNA-seq reads. Corrects Illumina sequencing errors in FASTQ data using Jellyfish2 bloom filters and adaptive kmer frequency thresholds. Handles non-uniform

2 shared topics • 2 shared operations

Sailfish — rapid mapping-based isoform quantification from RNA-seq reads. Uses quasi-mapping to estimate transcript abundance without full alignment. Provides TPM and estimated counts per transcript.

2 shared topics • 2 shared operations