Studies using refgenie

Here are some studies we have found that make use of refgenie in some way:

Dozmorov et al. (2021). Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines
GigaScience. DOI: /10.1093/gigascience/giab022

Leal-Calvo et al. (2021). A new paradigm for leprosy diagnosis based on host gene expression
bioRxiv. DOI: 10.1101/2021.07.30.454441

Rauscher et al. (2021). Patient-derived gene and protein expression signatures of NGLY1 deficiency
bioRxiv. DOI: 10.1101/2021.07.28.453930

Gudukbay et al. (2021). GYAN: Accelerating Bioinformatics Tools in Galaxy with GPU-Aware Computation Mapping
DOI: 10.1109/ipdpsw52791.2021.00037

Kupkova et al. (2021). Histone H3 lysine 27 acetylation profile undergoes two global shifts in undernourished children and suggests one-carbon metabolite insufficiency
medRxiv. DOI: 10.1101/2021.06.11.21258783

Toulmin et al. (2021). Type II alveolar cell MHCII improves respiratory viral disease outcomes while exhibiting limited antigen presentation
Nature Communications. DOI: 10.1038/s41467-021-23619-6

Gerber et al. (2021). Streamlining differential exon and 3′ UTR usage with diffUTR
BMC Bioinformatics. DOI: 10.1186/s12859-021-04114-7

Hasegawa et al. (2021). Clonal inactivation of telomerase promotes accelerated stem cell differentiation
bioRxiv. DOI: 10.1101/2021.04.28.441728

Mölder et al. (2021). Sustainable data analysis with Snakemake
F1000Research. DOI: 10.12688/f1000research.29032.2

Smith et al. (2021). PEPPRO: quality control and processing of nascent RNA profiling data
Genome Biology. DOI: 10.1186/s13059-021-02349-4

Smith et al. (2020). PEPATAC: An optimized ATAC-seq pipeline with serial alignments
bioRxiv. DOI: 10.1101/2020.10.21.347054

VijayKrishna et al. (2020). Expanding the Galaxy's reference data
bioRxiv. DOI: 10.1101/2020.10.09.327114

Zhou et al. (2020). CATA: a comprehensive chromatin accessibility database for cancer
bioRxiv. DOI: 10.1101/2020.05.16.099325