This repository contains the code used to derive the analyses presented in our paper. links: The scripts are presented in processing order.

01_annotation.R -> A R script that downloads the references used, and processes them for subsequent use.

02_indices.sh -> A shell script for downloading the genome as well as creating the alignment/quantification indices needed.

03_getPm.R -> A R script to estimate the probability matrices of each transcript to create observed feature counts.

04_get_bundles.R -> A R script to determine which genes need to be estimated together because they have overlapping mapping of reads.

05_simulate.R -> A R script that contains the code for the simulation studies of different methods using transcripts from protein-coding genes on chr1 and chr14.

06_CI.R -> A R script that contains the code for the simulation studies of the performance of our method's confidence intervals.

07_Geuvadis.sh -> A shell R script that details how we quantified the ERR188410 sample of the Geuvadis Consortium dataset using the methods covered in the paper.

08_simulate_rsem.R -> A R script that contains details how we evaluated the performance of the chosen models when ground truth is simulated using the RSEM estimates of sample ERR188410.

09_figures_tables.R -> A R script that creates the plots and tables presented (except the MA plots in the supplement).

10_graphics_MA.R -> A R script that produces the MA plots included in the supplement, as well as a short snippet to collect read lengths of samples in recount2.

11_run_all.R -> A R script that runs recountNNLS on all recount samples (minus TCGA and GTEX).

12_run_TCGA.R -> A R script that runs recountNNLS on the TCGA samples.

13_run_GTEX.R -> A R script that runs recountNNLS on the GTEX samples.

14_QCmetrics.R -> Short code snippet that we used checking how our fragment/read estimates correspond to overall mapped fragments/reads.

setting value
version R version 3.4.4 RC (2018-03-09 r74376) system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
tz US/Eastern
date 2018-05-10

Packages -------------------------------------------------------------------------------------------------------------- package * version date source
AnnotationDbi * 1.40.0 2017-11-01 Bioconductor
assertthat 0.2.0 2017-04-11 CRAN (R 3.4.0)
base * 3.4.4 2018-03-09 local
Biobase * 2.38.0 2017-11-01 Bioconductor
BiocGenerics * 0.24.0 2017-11-01 Bioconductor
BiocParallel 1.12.0 2017-11-01 Bioconductor
biomaRt 2.34.2 2018-01-21 Bioconductor
Biostrings * 2.46.0 2018-01-27 cran (@2.46.0)
bit 1.1-12 2014-04-09 CRAN (R 3.4.0)
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bitops 1.0-6 2013-08-17 CRAN (R 3.4.0)
blob 1.1.0 2017-06-17 CRAN (R 3.4.1)
BSgenome * 1.46.0 2017-11-01 Bioconductor
BSgenome.Hsapiens.UCSC.hg38 * 1.4.1 2017-05-26 Bioconductor
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DBI 0.8 2018-03-02 CRAN (R 3.4.3)
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devtools 1.13.5 2018-02-18 CRAN (R 3.4.3)
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GenomeInfoDb * 1.14.0 2017-11-01 Bioconductor
GenomeInfoDbData 1.0.0 2017-12-15 Bioconductor
GenomicAlignments 1.14.1 2018-01-27 cran (@1.14.1)
GenomicFeatures * 1.30.3 2018-02-03 Bioconductor
GenomicRanges * 1.30.3 2018-02-27 Bioconductor
graphics * 3.4.4 2018-03-09 local
grDevices * 3.4.4 2018-03-09 local
grid 3.4.4 2018-03-09 local
httr 1.3.1 2017-08-20 CRAN (R 3.4.1)
IRanges * 2.12.0 2017-11-01 Bioconductor
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magrittr 1.5 2014-11-22 CRAN (R 3.4.0)
Matrix 1.2-12 2017-11-30 CRAN (R 3.4.4)
matrixStats * 0.53.1 2018-02-11 CRAN (R 3.4.3)
memoise 1.1.0 2017-04-21 CRAN (R 3.4.0)
methods * 3.4.4 2018-03-09 local
parallel * 3.4.4 2018-03-09 local
pillar 1.2.1 2018-02-27 CRAN (R 3.4.3)
prettyunits 1.0.2 2015-07-13 CRAN (R 3.4.0)
progress 1.1.2 2016-12-14 CRAN (R 3.4.0)
R6 2.2.2 2017-06-17 CRAN (R 3.4.1)
Rcpp 0.12.15 2018-01-20 cran (@0.12.15)
RCurl 1.95-4.10 2018-01-04 CRAN (R 3.4.3)
recountNNLS * 0.99.7 2018-05-08 Github (jmf47/recountNNLS@9acad0b) recountNNLSdata * 0.99.8 2018-02-21 Bioconductor
rlang 0.2.0 2018-02-20 CRAN (R 3.4.3)
RMySQL 0.10.14 2018-02-26 CRAN (R 3.4.3)
Rsamtools * 1.30.0 2018-01-27 cran (@1.30.0)
RSQLite 2.0 2017-06-19 CRAN (R 3.4.1)
rtracklayer * 1.38.3 2018-01-24 Bioconductor
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stats * 3.4.4 2018-03-09 local
stats4 * 3.4.4 2018-03-09 local
stringi 1.1.6 2017-11-17 CRAN (R 3.4.2)
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tibble 1.4.2 2018-01-22 CRAN (R 3.4.3)
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withr 2.1.1 2017-12-19 CRAN (R 3.4.3)
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zlibbioc 1.24.0 2017-11-01 Bioconductor