databio/genomicdistributions issues and pull requests

#209 - getTssFromGTF

Issue - State: closed - Opened by Shukla04 9 months ago - 3 comments

#208 - Error installing GenomicDistributionsData

Issue - State: closed - Opened by nsheff 12 months ago - 3 comments

#207 - Dev

Pull Request - State: closed - Opened by kkupkova over 1 year ago

#206 - Custom partitions for a custom reference

Issue - State: closed - Opened by rrashford almost 2 years ago - 3 comments

#205 - Trying to use calcChromBinsRef for a custom genome fails

Issue - State: closed - Opened by aminakur almost 2 years ago - 5 comments

#204 - new release version bump

Pull Request - State: closed - Opened by kkupkova about 2 years ago

#203 - add citation file

Pull Request - State: closed - Opened by kkupkova about 2 years ago

#202 - catch up with master

Pull Request - State: closed - Opened by kkupkova about 2 years ago

#201 - Determining which regions were labeled with each partition name

Issue - State: open - Opened by rrashford about 2 years ago - 1 comment
Labels: enhancement

#200 - v 1.5.5 build warning fix

Pull Request - State: closed - Opened by kkupkova over 2 years ago

#199 - bug fix - partition list

Pull Request - State: closed - Opened by kkupkova over 2 years ago - 1 comment

#198 - v1.5.3: bug fixes

Pull Request - State: closed - Opened by kkupkova over 2 years ago

#197 - v1.5.2

Pull Request - State: closed - Opened by kkupkova over 2 years ago

#196 - mm10 genome not available in GenomicDistributions or ExperimentHub

Issue - State: closed - Opened by rrashford over 2 years ago - 3 comments

#195 - 1.5.1 bug fix in calcSummarySignal for mm10

Pull Request - State: closed - Opened by kkupkova over 2 years ago

#194 - get up to date with master after biocondutor update

Pull Request - State: closed - Opened by kkupkova over 2 years ago

#193 - corrected vignette

Pull Request - State: closed - Opened by kkupkova over 2 years ago

#192 - v1.3.5

Pull Request - State: closed - Opened by kkupkova over 2 years ago

#191 - v1.3.4

Pull Request - State: closed - Opened by kkupkova over 2 years ago

#190 - Support for organisms such as Plasmodium Falciparum with gffs/gtfs that dont have 'gene_biotype' in the 9th column

Issue - State: closed - Opened by JesseRop almost 3 years ago - 5 comments

#189 - Genomic partitions plot frequencies not per set

Issue - State: closed - Opened by ChristelKrueger almost 3 years ago - 2 comments

#188 - Release

Pull Request - State: closed - Opened by nsheff almost 3 years ago

#187 - CFRIF updates

Pull Request - State: closed - Opened by nsheff almost 3 years ago - 1 comment

#186 - increase version number - correct

Pull Request - State: closed - Opened by kkupkova almost 3 years ago

#185 - Update full-power.Rmd

Pull Request - State: closed - Opened by kkupkova almost 3 years ago

#184 - 1.3.1 update NEWS

Pull Request - State: closed - Opened by kkupkova almost 3 years ago

#183 - Version 1.3.1

Pull Request - State: closed - Opened by kkupkova almost 3 years ago

#182 - Dev jose

Pull Request - State: closed - Opened by joseverdezoto almost 3 years ago

#181 - Dev jose

Pull Request - State: closed - Opened by joseverdezoto almost 3 years ago

#180 - make an option to plot different datasets by different colors

Issue - State: open - Opened by kkupkova almost 3 years ago - 3 comments
Labels: enhancement

#179 - in plotQTHist, numbers param doesn't always work

Issue - State: closed - Opened by nsheff almost 3 years ago - 4 comments
Labels: bug

#178 - plotQTHist quantile param name

Issue - State: closed - Opened by nsheff almost 3 years ago

#177 - Confusion about branches

Issue - State: closed - Opened by nsheff almost 3 years ago - 1 comment

#176 - Deprecation warning

Issue - State: closed - Opened by nsheff almost 3 years ago - 2 comments

#175 - Build reference data examples require too large of downloads.

Issue - State: closed - Opened by nsheff almost 3 years ago - 2 comments

#174 - Assignment operator

Issue - State: closed - Opened by nsheff almost 3 years ago - 1 comment

#173 - Distance to TSSs is wrong

Issue - State: closed - Opened by nsheff almost 3 years ago - 5 comments

#172 - Nearest Genes Function

Pull Request - State: open - Opened by nleroy917 almost 3 years ago - 28 comments

#171 - plotChromBins - option to change limit of y-axes

Pull Request - State: closed - Opened by tgstoecker almost 3 years ago - 2 comments

#170 - Nearest Genes Function

Pull Request - State: closed - Opened by nleroy917 about 3 years ago - 3 comments

#169 - Add corrected neighbor dist, nearestNeighbors, doc changes

Pull Request - State: closed - Opened by joseverdezoto about 3 years ago

#168 - Add calcNearestGenes Function

Pull Request - State: closed - Opened by nleroy917 about 3 years ago - 13 comments

#167 - mm10 specificity plots

Pull Request - State: closed - Opened by kkupkova about 3 years ago

#166 - update documentation

Pull Request - State: closed - Opened by kkupkova over 3 years ago

#165 - remove all bpProportion=T examples to avoid build error

Pull Request - State: closed - Opened by kkupkova over 3 years ago

#164 - one more bioconductor windows build fix

Pull Request - State: closed - Opened by kkupkova over 3 years ago

#163 - fix build error on Windows (Bioconductor issue only)

Pull Request - State: closed - Opened by kkupkova over 3 years ago

#162 - v1.1.5

Pull Request - State: closed - Opened by kkupkova over 3 years ago

#161 - nicer dinuc. plots and avoid build error in Bioconductor

Pull Request - State: closed - Opened by kkupkova over 3 years ago

#160 - update vignettes, typo

Pull Request - State: closed - Opened by kkupkova over 3 years ago

#159 - update 3.6 with version 1.1.2

Pull Request - State: closed - Opened by kkupkova over 3 years ago

#158 - #133 add dinucleotide frequency calculation

Pull Request - State: closed - Opened by kkupkova over 3 years ago

#157 - Calcdinuclfreq

Pull Request - State: closed - Opened by nsheff over 3 years ago

#156 - update NEWS

Pull Request - State: closed - Opened by kkupkova over 3 years ago

#155 - fix version number - 1.1.1

Pull Request - State: closed - Opened by kkupkova over 3 years ago

#154 - Add custom reference data vignette

Pull Request - State: closed - Opened by stolarczyk over 3 years ago

#153 - Expected tissue specificity plots

Issue - State: open - Opened by kkupkova over 3 years ago - 6 comments
Labels: enhancement

#152 - reduce memory in `plotOpenSignal`

Pull Request - State: closed - Opened by xuebingjie1990 over 3 years ago - 2 comments

#151 - couple edits to reduce neighb dist mem consumption

Pull Request - State: closed - Opened by joseverdezoto over 3 years ago

#150 - Kristyna dev

Pull Request - State: closed - Opened by kkupkova over 3 years ago

#149 - vignette edits

Pull Request - State: closed - Opened by kkupkova over 3 years ago

#148 - Release 1.2.0

Pull Request - State: closed - Opened by nsheff over 3 years ago - 3 comments

#147 - Bring 3.6 version up-to-date with latest updates

Pull Request - State: closed - Opened by nsheff over 3 years ago

#146 - add stacked bar plot option to partition plots

Pull Request - State: closed - Opened by kkupkova over 3 years ago

#145 - GenomicDistributions not compatible with R >=4.0?

Issue - State: closed - Opened by steph-e over 3 years ago - 2 comments

#144 - relevel chromosomes

Pull Request - State: closed - Opened by kkupkova over 3 years ago

#143 - reduce plotting time

Pull Request - State: closed - Opened by xuebingjie1990 over 3 years ago

#142 - increase GC content calculation performance

Issue - State: closed - Opened by stolarczyk over 3 years ago - 6 comments
Labels: likely-fixed

#141 - Reduce run time

Issue - State: closed - Opened by xuebingjie1990 over 3 years ago - 7 comments
Labels: enhancement

#140 - Reduce memory use

Issue - State: open - Opened by xuebingjie1990 over 3 years ago - 2 comments
Labels: enhancement

#139 - Add enhancers to partition plots

Issue - State: closed - Opened by kkupkova over 3 years ago - 1 comment
Labels: enhancement, docs

#138 - fix wrong violin plot inputs

Pull Request - State: closed - Opened by kkupkova over 3 years ago

#137 - Add feature overlap bar plot

Issue - State: closed - Opened by kkupkova over 3 years ago
Labels: improvement

#136 - expected feature overlap based on bp of each feature

Pull Request - State: closed - Opened by kkupkova over 3 years ago

#135 - Violin plots

Pull Request - State: closed - Opened by kkupkova over 3 years ago

#134 - Tss order

Pull Request - State: closed - Opened by kkupkova over 3 years ago

#133 - Dinucleotide frequency

Issue - State: closed - Opened by kkupkova over 3 years ago
Labels: enhancement

#132 - Proportional feature overlap

Issue - State: closed - Opened by kkupkova over 3 years ago
Labels: improvement

#131 - Violin plots for cell type

Issue - State: closed - Opened by kkupkova over 3 years ago
Labels: plot-type

#130 - Tss Order Sorted

Pull Request - State: closed - Opened by ser9gj over 3 years ago - 1 comment

#129 - Help with Sorting using nbins

Issue - State: closed - Opened by ser9gj over 3 years ago - 3 comments

#128 - fixed problem with TSS distances

Pull Request - State: closed - Opened by kkupkova almost 4 years ago

#127 - Tss dist bug

Pull Request - State: closed - Opened by kkupkova almost 4 years ago

#126 - Updated installation instructions and reduced repository size

Pull Request - State: closed - Opened by kkupkova about 4 years ago

#125 - Chromosome distribution plot not sorted correctly when 2 regions sets are not in all chromosomes

Issue - State: closed - Opened by kkupkova about 4 years ago
Labels: bug

#124 - Rainfall plots

Issue - State: open - Opened by nsheff about 4 years ago
Labels: enhancement

#123 - ranking distance to tss plots

Issue - State: closed - Opened by nsheff about 4 years ago

#122 - update install instructions

Issue - State: closed - Opened by nsheff about 4 years ago - 1 comment

#121 - Clean up repository history

Issue - State: closed - Opened by nsheff about 4 years ago - 2 comments

#120 - Add functions for computing and plotting dinucleotide frequencies

Pull Request - State: closed - Opened by jstubbs01 about 4 years ago - 27 comments

#119 - open chromatin function updated

Pull Request - State: closed - Opened by kkupkova about 4 years ago - 11 comments

#117 - Vignettes needs to update

Issue - State: closed - Opened by xuebingjie1990 about 4 years ago - 20 comments

#114 - Bioconductor submission status

Issue - State: closed - Opened by joseverdezoto over 4 years ago - 5 comments

#113 - plotOpenSignal suggestions

Issue - State: closed - Opened by nsheff over 4 years ago - 4 comments

#111 - Missing reference data

Issue - State: closed - Opened by jpsmith5 over 4 years ago - 18 comments

#107 - openSignalMatrix maximum is 0.6279

Issue - State: closed - Opened by nsheff over 4 years ago - 4 comments

#100 - warning in cumulative partitions distribution calculation

Issue - State: closed - Opened by joseverdezoto over 4 years ago - 4 comments
Labels: likely-fixed

#99 - remove expected and cumul part stray printouts

Pull Request - State: closed - Opened by joseverdezoto over 4 years ago

#98 - fix faulty unit test for travis checks

Pull Request - State: closed - Opened by joseverdezoto over 4 years ago

#97 - update docs

Pull Request - State: closed - Opened by joseverdezoto over 4 years ago

GitHub / databio/genomicdistributions issues and pull requests