Package: APAlyzer 1.19.0

Ruijia Wang

APAlyzer: A toolkit for APA analysis using RNA-seq data

Perform 3'UTR APA, Intronic APA and gene expression analysis using RNA-seq data.

Authors:Ruijia Wang [cre, aut], Bin Tian [aut], Wei-Chun Chen [aut]

APAlyzer_1.19.0.tar.gz
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APAlyzer.pdf |APAlyzer.html✨
APAlyzer/json (API)
NEWS

# Install 'APAlyzer' in R:

install.packages('APAlyzer', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rjwangbioinfo/apalyzer/issues

On BioConductor:APAlyzer-1.19.0(bioc 3.20)APAlyzer-1.18.0(bioc 3.19)

bioconductor-package

12 exports 0.61 score 113 dependencies 4 mentions

Last updated 2 months agofrom:efcd08d0c2

Exports:APABox APAdiff APAVolcano download_testbam GENEXP_CDS PAS2GEF PASEXP_3UTR PASEXP_IPA REF3UTR REF4PAS REFCDS ThreeMostPairBam

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cli codetools colorspace cpp11 crayon curl data.table DBI DelayedArray DESeq2 digest dplyr fansi farver fastmap fdrtool formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggrepel glue gtable httr HybridMTest IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr plyr png purrr R.cache R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RcppArmadillo RCurl repmis restfulr Rhtslib rjson rlang Rsamtools RSQLite Rsubread rtracklayer S4Arrays S4Vectors scales snow SparseArray stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr XML XVector yaml zlibbioc

APAlyzer: A toolkit for APA analysis using RNA-seq data

Ruijia Wang, Bin Tian

Rendered fromAPAlyzer.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2022-03-01
Started: 2019-07-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
APABox, APA RED Box plotting	APABox
APAdiff, calculate delta relative expression (RED) and statistics significance between two sample groups	APAdiff
APAVolcano, APA Volcano plotting	APAVolcano
download_testbam, download bam files of mouse testis and heart	download_testbam
GENEXP_CDS, count reads mapped to CDS regions and calculate TPM for coding gene	GENEXP_CDS
PAS2GEF, build reference regions for 3'UTR PASs	PAS2GEF
PASEXP_3UTR, calculate relative expression of aUTR and cUTR regions	PASEXP_3UTR
PASEXP_IPA, calculate relative expression of IPA regions	PASEXP_IPA
REF3UTR, build reference regions for 3'UTR PASs	REF3UTR
REF4PAS, build reference regions for 3'UTR and Intronic PAS using dataframe formated input	REF4PAS
REFCDS, build reference regions for CDS of protein coding genes	REFCDS
ThreeMostPairBam, extract 3 prime most alignment of a paired-end bam file	ThreeMostPairBam

Usage by other packages (reverse dependencies)