Merge pull request #21 from BIMSBbioinfo/dev2

ciRcus v0.1.4

.Rbuildignore

@@ -3,3 +3,4 @@
 ^\.git
 ^\.gitignore
 ^\.travis\.yml$
+^CHANGELOG\.md$

.gitignore

@@ -1,5 +1,3 @@
 .Rproj.user
 .Rhistory
 .RData
-data/
-man/

.travis.yml

@@ -0,0 +1,21 @@
+# Sample .travis.yml for R projects.
+#
+# See README.md for instructions, or for more configuration options,
+# see the wiki:
+#   https://github.com/craigcitro/r-travis/wiki
+
+# See https://docs.travis-ci.com/user/languages/r/#Basic-configuration
+language: r
+cache: packages
+
+# See https://docs.travis-ci.com/user/languages/r/#R-Versions
+r:
+#  - oldrel
+  - release
+  - devel
+
+sudo: required
+bioc_required: true
+
+#after_success:
+#- Rscript -e 'covr::codecov()'

CHANGELOG.md

@@ -0,0 +1,44 @@
+ciRcus 0.1.4
+------------
+
+NEW FEATURES
+
+* CIRI2 support
+* WBcel235 genome assembly supported
+* QC plot for total vs. unique reads
+
+IMPROVEMENTS AND BUG FIXES
+
+* sample order from colData is not broken by summarizeCircs
+* system.file call fixed in README
+
+
+ciRcus 0.1.3
+------------
+NEW FEATURES
+
+* find_circ2 supported
+
+IMPROVEMENTS AND BUG FIXES
+
+* different coordinate indexing in input and annotation
+  will be automatically detected and fixed
+* lots of under-the-hood improvements
+
+ciRcus 0.1.2
+------------
+NEW FEATURES
+
+* find_circ.py v1.2 supported
+
+ciRcus 0.1.1
+--------------
+NEW FEATURES
+
+* input is loaded into a SummarizedExperiment object
+* basic circBase interaction
+
+
+IMPROVEMENTS AND BUG FIXES
+
+* unit tests

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ciRcus
 Type: Package
 Title: Annotation, analysis and visualization of circRNA data
-Version: 0.1.3
+Version: 0.1.4
 Author: Petar Glazar [aut, cre], Vedran Franke [aut, cre]
 Maintainer: Petar Glazar <petar.glazar@gmail.com>, Vedran Franke
     <vedran.franke@gmail.com>
@@ -15,8 +15,10 @@ LazyLoad: yes
 VignetteBuilder: knitr
 biocViews: Annotation, HighThroughputSequencing, Visualization
 Depends:
-    R (>= 3.0.0)
+    R (>= 3.0.0),
+    methods
 Imports:
+    AnnotationDbi,
     AnnotationHub,
     biomaRt,
     data.table,
@@ -26,6 +28,7 @@ Imports:
     ggplot2,
     hash,
     IRanges,
+    RColorBrewer,
     RMySQL,
     S4Vectors,
     stringr,

NAMESPACE

@@ -1,12 +1,13 @@
 # Generated by roxygen2: do not edit by hand
 
 export(AnnotateRanges)
+export(MungeColumn)
+export(ProcessLinear)
 export(annotPie)
 export(annotateCircs)
 export(annotateFlanks)
 export(annotateHostGenes)
 export(annotateJunctions)
-export(circHist)
 export(circLinRatio)
 export(getStudiesList)
 export(gtf2sqlite)
@@ -15,19 +16,32 @@ export(loadAnnotation)
 export(readCircs)
 export(resTable)
 export(summarizeCircs)
+export(testCoordinateIndexing)
+export(uniqReadsQC)
 import(AnnotationHub)
 import(DBI)
-import(GenomicFeatures)
-import(GenomicRanges)
-import(IRanges)
 import(RMySQL)
 import(S4Vectors)
 import(SummarizedExperiment)
-import(biomaRt)
-import(data.table)
 import(ggplot2)
-import(hash)
+import(methods)
 import(stringr)
 importFrom(AnnotationDbi,loadDb)
 importFrom(AnnotationDbi,saveDb)
+importFrom(GenomicFeatures,makeTxDbFromGRanges)
+importFrom(GenomicRanges,makeGRangesFromDataFrame)
+importFrom(GenomicRanges,reduce)
+importFrom(GenomicRanges,resize)
+importFrom(IRanges,findOverlaps)
 importFrom(RColorBrewer,brewer.pal)
+importFrom(biomaRt,getBM)
+importFrom(biomaRt,useDataset)
+importFrom(biomaRt,useMart)
+importFrom(data.table,data.table)
+importFrom(data.table,dcast.data.table)
+importFrom(data.table,fread)
+importFrom(data.table,rbindlist)
+importFrom(data.table,set)
+importFrom(data.table,setnames)
+importFrom(hash,hash)
+importFrom(hash,keys)