GRAND-SLAM is a tool to estimate new-to-total RNA (NTR) ratios from SLAM-seq data and other nucleotide conversion RNA-seq approaches. Provided with mapped reads of all samples (replicates, conditions, etc.) or cells (in case of single cell sequencing) from an experiment, it generates a table containing read counts, NTRs and their posterior distributions (reflecting uncertainty in estimating NTRs) of all sample and all genes.

GRAND-SLAM is part of the GEDI toolkit and available at: https://github.com/erhard-lab/gedi

Jürges C, Dölken L, Erhard F. Dissecting newly transcribed and old RNA using GRAND-SLAM. Bioinformatics. Jul 2018. 34(13):i218-i226. (»DOI:10.1093/bioinformatics/bty256) PDF

Erhard F, Baptista MAP, Krammer T, Hennig T, Lange M, Arampatzi P, Jürges CS, Theis FJ, Saliba AE, Dölken L. scSLAM-seq reveals core features of transcription dynamics in single cells. Nature. Jul 2019. 571(7765):419-423. (»DOI:10.1038/s41586-019-1369-y) PDF

Erhard F. Two-Step Parameter Estimation for Read Feature Models. Künstl Intell. Jan 2024.
(»DOI:10.1007/s13218-023-00821-w) PDF 

grandRescue is a software to circumvent mappability problems and correct for 4sU-induced quantification bias in SLAM-seq data and other nucleotide conversion RNA-seq approaches. To achieve this, grandRescue aligns previously unmappable reads in a T-to-C mismatch independent manner.

GrandRescue is available at https://github.com/erhard-lab/grandRescue

Berg K, Lodha M, Delazer I, Bartosik K, Garcia YC, Hennig T, Wolf E, Dölken L, Lusser A, Prusty BK, Erhard F. Correcting 4sU induced quantification bias in nucleotide conversion RNA-seq data. Nucleic Acids Res.  Apr 2024. 52(7):e35.
(»DOI:10.1093/nar/gkae120) PDF 

After primary processing by GRAND-SLAM, the R package grandR provides specialized tools for downstream analyses of SLAM-seq data. grandR provides a comprehensive toolbox for quality control, kinetic modeling, differential gene expression analysis and visualization of such data. It provides an interface to Seurat for single cell analyses and a web based visualization via shiny.

GrandR is available on CRAN and at https://grandr.erhard-lab.de/

Rummel T, Sakellaridi L, Erhard F. grandR: a comprehensive package for nucleotide conversion RNA-seq data analysis. Nat Commun. Jun 2023. 14(1):3559.
(»DOI:10.1038/s41467-023-39163-4) PDF

iTiSS (integrated Transcriptional start site caller) is a method to identify transcriptional start sites (TiSS) from various TiSS-profiling experiments with an additional integrative module to combine and remove artefactual TiSS called in single data sets.

iTiSS is available at https://github.com/erhard-lab/iTiSS

Jürges CS, Dölken L, Erhard F. Integrative transcription start site identification with iTiSS. Bioinformatics. Sep 2021. 37(18):3056-3057. (»DOI:10.1093/bioinformatics/btab170) PDF

LFC is a tool for estimating log fold changes and pseudocounts for RNA-seq experiments. It does not only provide points estimates, but computes posterior probabilities of log fold changes.

LFC is available in CRAN and at https://github.com/erhard-lab/lfc

Erhard F, Zimmer R. Count ratio model reveals bias affecting NGS fold changes. Nucleic Acids Res. Jul 2015. 43(20):e136-e136. (»DOI:10.1093/nar/gkv696) PDF

Erhard F. Estimating pseudocounts and fold changes for digital expression measurements. Bioinformatics. Dec. 2018.34(23):4054-4063. (»DOI:10.1093/bioinformatics/bty471) PDF