Bioc Release: 1.1

This is the release used for our article (Bhardwaj et. al. 2019, Nature Comm)

just better

(almost) ready for submission to bioconductor.

1. Better PCR dup removal (taking strand into account).
2. Better TSS calling (full strand specificity + sliding window + other improvements)
3. Vignettes ready
4. Testing implemented
5. Plot precision more accurate (CDF calculated on all data, not just from the given range)
6. Many improvements to code structure and checks added.

packed and pumped

Probably the last release before the bioconductor submission.

1. S4 implementation
2. Getting rid of C code and simplified the trimming/demultiplexing
3. New plotting wrappers
4. Fixed many issues and passed devtools::check

0.2

Added new function to get gene counts using the TSS data.

Probably the last release before the S4 implementation..

First working end-to-end CAGE analysis workflow

This release has functions for end-to-end CAGE analysis workflow, including functions for processing MAPCap data.

Functions :

1. Trim barcodes from MAPCap fastq files and keep in header.
2. Map any paired-end CAGE data.
3. Post mapping de-multiplexing of the BAM file using initially trimmed and kept barcodes.
4. PCR de-duplication using UMIs and mapping position of reads in genomic bins.
5. New TSS detection method that's shown to work nicely with sharp peaks (comparison with other data/programs pending).
6. Differential TSS detection using an RNAseq-like approach.
7. Annotation of detected TSS.
8. QC plot for precision of detected TSS.
9. A wrapper of old method of TSS calling (to be removed in future).

Major changes to the software are pending. I shall follow the semantic versioning rule with releases.