Files in Maxim-Ivanov/TranscriptomeReconstructoR
Data-driven Annotation of the Transcriptome
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/Adjust_exons.R
R/Call_tag_clusters.R
R/Call_transcript.R
R/Extend_long_reads.R
R/Find_alignment_errors.R
R/Load_BAM_files.R
R/Process_nascent_data.R
R/Refine_by_annotation.R
R/Utility_functions.R
README.md
TranscriptomeReconstructoR.Rproj
Utility_functions.R
doc/TranscriptomeReconstructoR.R
doc/TranscriptomeReconstructoR.Rmd
doc/TranscriptomeReconstructoR.html
inst/extdata/cage_rep1_filt.bam
inst/extdata/cage_rep2_filt.bam
inst/extdata/cage_rep3_filt.bam
inst/extdata/ont_rep1_filt.bam
inst/extdata/ont_rep2_filt.bam
inst/extdata/ont_rep3_filt.bam
inst/extdata/ont_rep4_filt.bam
inst/extdata/pat_rep1_filt.bam
inst/extdata/pat_rep2_filt.bam
inst/extdata/pat_rep3_filt.bam
inst/extdata/planet_rep1_filt.bam
inst/extdata/planet_rep2_filt.bam
man/adjust_exons_of_long_reads.Rd
man/call_TCs.Rd
man/call_transcribed_intervals.Rd
man/call_transcripts_and_genes.Rd
man/detect_alignment_errors.Rd
man/extend_long_reads_to_TSS_and_PAS.Rd
man/flip_strand_info.Rd
man/load_BAM_files.Rd
man/merge_GRanges.Rd
man/process_nascent_intervals.Rd
man/refine_transcripts_by_annotation.Rd
man/save_GRanges_as_bedGraph.Rd
man/write_grl_as_bed12.Rd
vignettes/.gitignore
vignettes/Fig_01.png
vignettes/Fig_02.png
vignettes/Fig_03.png
vignettes/Fig_04.png
vignettes/Fig_05.png
vignettes/Fig_06.png
vignettes/Fig_07.png
vignettes/Fig_08.png
vignettes/Fig_09.png
vignettes/Fig_10.png
vignettes/Fig_11.png
vignettes/TranscriptomeReconstructoR.Rmd
vignettes/bibliography.bib
