├── .DS_Store ├── At_rRNA_AGIs.txt ├── ChIP ├── README.md └── chip-seq_v0.1.sh ├── DNA └── dna_wgs_pipe.v1.sh ├── MethylC ├── 100bp_dmr_merge.r ├── 100bp_dmrs.v0.1.sh ├── 100bp_heatmap.sh ├── 100bp_wig_to_dmrs.r ├── 5mC_rates.sh ├── BS-SNPer.sh ├── DSS_file_prep.r ├── README.md ├── bed_to_rel_dist.sh ├── dmr_merge.r ├── dss_calling.r ├── merge_wigs.r ├── met_signatures.sh ├── methimpute.r ├── pca_wigs.r ├── rel_methylation_plots.r ├── rel_methylation_plots_v2.r ├── scatman_smooth.sh ├── smooth_scat.r ├── wgbs_cov_to_TDF.sh ├── wgbs_custom_bins.sh ├── wgbs_pipeline_v0.4.sh ├── wgbs_pipeline_v0.5.sh ├── wgbs_pipeline_v0.6.sh └── wgbs_pipeline_v0.7.sh ├── Os-IRGSP_annotation.sh ├── README.md ├── RNA ├── BAM_to_5p_bigWigs.sh ├── BAM_to_CTRD.counts.sh ├── BAM_to_EJC.counts.sh ├── BAM_to_EJC.sh ├── BAM_to_ESI.sh ├── BAM_to_STOP.sh ├── BAM_to_TSI.sh ├── BAM_to_bedgraph.sh ├── BAM_to_bedgraph_5p.sh ├── BAM_to_bigWig.sh ├── BAM_to_wigs.sh ├── ESI_calculation.r ├── README.md ├── STAR_pipe_v1.sh ├── SUPPA_pipe_v1.sh ├── SUPPA_pipe_v2.sh ├── TSI_calculation.r ├── featureCounts_to_edgeR.r ├── featureCounts_v1.sh ├── featureCounts_v2.sh ├── featureCounts_v3-gtf.sh ├── get_peak_length.sh ├── gmuct_pipe_v1.sh ├── graft-nad-seq.sh ├── kallisto_pipe_v1.sh ├── macs_peaks.sh ├── nadBAM_to_ADPRC_sites.sh ├── pare_pipe_v1.sh ├── rel_expression_plots.r ├── rel_expression_plots_ejc.r ├── rel_expression_plots_nad.r ├── rel_expression_plots_stop.r ├── smrna_pipe_v1.sh ├── split_file.R ├── stringtie_extract_tpm.r ├── stringtie_pipe_v1.sh ├── stringtie_pipe_v2.sh ├── subread_pipe_v1.sh ├── subread_pipe_v2.sh ├── subread_pipe_v3.sh ├── total_expression.r ├── trim_5p_graft_nad.r └── trim_fastq.sh ├── TAIR10_annotation.sh ├── TruSeq-adapters.fa ├── VennPieces.R ├── araport11_assemble.sh ├── average_cov.sh ├── bashrc ├── gene_to_gene_anno.sh ├── osa1_r7_annotation.sh ├── pe_insert_size.sh ├── project_workflows ├── Exp555_cordycepin_comparison.Rmd ├── Ganguly_2025_abh1_diffSegR │ ├── diffsegR_WT-NvsC_gmuct_3p_v1.r │ ├── diffsegR_WT-NvsC_gmuct_3p_v1_stranded.r │ ├── diffsegR_WT-NvsC_gmuct_5p_v1.r │ ├── diffsegR_WT-NvsC_gmuct_5p_v1_stranded.r │ ├── diffsegR_abh1-CvsWT-C_gmuct_3p_v1.r │ ├── diffsegR_abh1-CvsWT-C_gmuct_3p_v1_stranded.r │ ├── diffsegR_abh1-CvsWT-C_gmuct_5p_v1.r │ ├── diffsegR_abh1-CvsWT-C_gmuct_5p_v1_stranded.r │ ├── diffsegR_abh1-NvsWT-N_gmuct_3p_v1.r │ ├── diffsegR_abh1-NvsWT-N_gmuct_3p_v1_stranded.r │ ├── diffsegR_abh1-NvsWT-N_gmuct_5p_v1.r │ └── diffsegR_abh1-NvsWT-N_gmuct_5p_v1_stranded.r ├── HL_RNAseq_vs_protein-stability.Rmd ├── RNA_protein_alignments.Rmd ├── Smith_2024_PlantJournal.Rmd ├── covid19_qPCR_analysis.Rmd ├── covid19_qPCR_analysis.html ├── diffsegR_v2 │ ├── GMUCT_cyto_dxo1vsWT_stranded_counts.r │ ├── GMUCT_nuc_dxo1vsWT_stranded_counts.r │ ├── GRAFT-NAD_WTvsnudt19.r │ ├── diffsegR_abh1-NvsWT-N_gmuct_3p.r │ └── diffsegR_abh1-NvsWT-N_gmuct_5p.r ├── lowD_5mC_dendrograms_281019.R ├── lowD_SNP_dendrograms_281019.R └── 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