goekelab/proactiv issues and pull requests

#55 - Filtering Steps for proActiv Analysis

Issue - State: open - Opened by lucianhu 3 months ago

#55 - Filtering Steps for proActiv Analysis

Issue - State: open - Opened by lucianhu 3 months ago

#55 - Filtering Steps for proActiv Analysis

Issue - State: open - Opened by lucianhu 3 months ago - 1 comment

#54 - mean read count data

Issue - State: closed - Opened by kenasada 4 months ago - 1 comment

#54 - mean read count data

Issue - State: closed - Opened by kenasada 4 months ago - 1 comment

#54 - mean read count data

Issue - State: closed - Opened by kenasada 4 months ago - 1 comment

#53 - unable to create promotor annotation for a non-model organism

Issue - State: closed - Opened by ShenTTT 6 months ago - 7 comments

#53 - unable to create promotor annotation for a non-model organism

Issue - State: closed - Opened by ShenTTT 6 months ago - 7 comments

#53 - unable to create promotor annotation for a non-model organism

Issue - State: closed - Opened by ShenTTT 6 months ago - 7 comments

#52 - Does getAlternativePromoters function work properly?

Issue - State: closed - Opened by Tianle-Li 11 months ago

#52 - Does getAlternativePromoters function work properly?

Issue - State: closed - Opened by Tianle-Li 11 months ago

#52 - Does getAlternativePromoters function work properly?

Issue - State: closed - Opened by Tianle-Li 11 months ago

#51 - Couldn't find a BSgenome data package that matches genome assembly: oryCun2.0

Issue - State: closed - Opened by houruiyan about 1 year ago - 2 comments

#51 - Couldn't find a BSgenome data package that matches genome assembly: oryCun2.0

Issue - State: closed - Opened by houruiyan about 1 year ago - 2 comments

#51 - Couldn't find a BSgenome data package that matches genome assembly: oryCun2.0

Issue - State: closed - Opened by houruiyan about 1 year ago - 2 comments

#50 - core dumped

Issue - State: closed - Opened by houruiyan about 1 year ago - 1 comment

#50 - core dumped

Issue - State: closed - Opened by houruiyan about 1 year ago - 1 comment

#50 - core dumped

Issue - State: closed - Opened by houruiyan about 1 year ago - 1 comment

#49 - What is the mean of names(genomeStyles()) ?

Issue - State: closed - Opened by houruiyan about 1 year ago - 2 comments

#49 - What is the mean of names(genomeStyles()) ?

Issue - State: closed - Opened by houruiyan about 1 year ago - 2 comments

#49 - What is the mean of names(genomeStyles()) ?

Issue - State: closed - Opened by houruiyan about 1 year ago - 2 comments

#48 - Error in `[[<-`(`tmp`, name, value = new("SimpleIntegerList", elementType = "integer",

Issue - State: closed - Opened by mmpust over 1 year ago - 4 comments

#48 - Error in `[[<-`(`tmp`, name, value = new("SimpleIntegerList", elementType = "integer",

Issue - State: closed - Opened by mmpust over 1 year ago - 4 comments

#48 - Error in `[[<-`(`tmp`, name, value = new("SimpleIntegerList", elementType = "integer",

Issue - State: closed - Opened by mmpust over 1 year ago - 4 comments

#47 - plotPromoters function not available in latest version

Issue - State: open - Opened by notthathime over 1 year ago - 1 comment

#47 - plotPromoters function not available in latest version

Issue - State: open - Opened by notthathime over 1 year ago - 1 comment

#47 - plotPromoters function not available in latest version

Issue - State: open - Opened by notthathime over 1 year ago - 1 comment

#46 - A little question about internal promoter^_^

Issue - State: open - Opened by CuteGold0407 over 1 year ago

#46 - A little question about internal promoter^_^

Issue - State: open - Opened by CuteGold0407 over 1 year ago

#46 - A little question about internal promoter^_^

Issue - State: open - Opened by CuteGold0407 over 1 year ago

#45 - Error in EstimateSizeFactorsForMatrix: at least one zero

Issue - State: open - Opened by notthathime almost 2 years ago - 1 comment

#45 - Error in EstimateSizeFactorsForMatrix: at least one zero

Issue - State: open - Opened by notthathime almost 2 years ago - 1 comment

#45 - Error in EstimateSizeFactorsForMatrix: at least one zero

Issue - State: open - Opened by notthathime almost 2 years ago - 1 comment

#44 - calculatePromoterReadCounts were not running

Issue - State: open - Opened by GuangyaoL almost 2 years ago - 1 comment

#44 - calculatePromoterReadCounts were not running

Issue - State: open - Opened by GuangyaoL almost 2 years ago - 1 comment

#44 - calculatePromoterReadCounts were not running

Issue - State: open - Opened by GuangyaoL almost 2 years ago - 1 comment

#43 - Identification of cancer-associated promoters

Issue - State: open - Opened by alejandrogzi about 2 years ago

#43 - Identification of cancer-associated promoters

Issue - State: open - Opened by alejandrogzi about 2 years ago

#43 - Identification of cancer-associated promoters

Issue - State: open - Opened by alejandrogzi about 2 years ago

#42 - could not find function "getAlternativePromoters"

Issue - State: closed - Opened by wenmm over 2 years ago - 1 comment

#42 - could not find function "getAlternativePromoters"

Issue - State: closed - Opened by wenmm over 2 years ago - 1 comment

#42 - could not find function "getAlternativePromoters"

Issue - State: closed - Opened by wenmm over 2 years ago - 1 comment

#41 - Some question about getAlternativePromoters()

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

#41 - Some question about getAlternativePromoters()

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

#41 - Some question about getAlternativePromoters()

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

#40 - used for 10x data

Issue - State: closed - Opened by houruiyan almost 3 years ago - 2 comments
Labels: question

#40 - used for 10x data

Issue - State: closed - Opened by houruiyan almost 3 years ago - 2 comments
Labels: question

#40 - used for 10x data

Issue - State: closed - Opened by houruiyan almost 3 years ago - 2 comments
Labels: question

#39 - cannot find extdata/testdata/bam

Issue - State: closed - Opened by houruiyan almost 3 years ago - 2 comments
Labels: question

#39 - cannot find extdata/testdata/bam

Issue - State: closed - Opened by houruiyan almost 3 years ago - 2 comments
Labels: question

#39 - cannot find extdata/testdata/bam

Issue - State: closed - Opened by houruiyan almost 3 years ago - 2 comments
Labels: question

#38 - Getting active/inactive and major/minor promoters when no condition is specified

Issue - State: open - Opened by elenichri almost 3 years ago - 1 comment

#38 - Getting active/inactive and major/minor promoters when no condition is specified

Issue - State: open - Opened by elenichri almost 3 years ago - 1 comment

#38 - Getting active/inactive and major/minor promoters when no condition is specified

Issue - State: open - Opened by elenichri almost 3 years ago - 1 comment

#37 - fix a typo in doc

Pull Request - State: closed - Opened by lu000016 about 3 years ago

#37 - fix a typo in doc

Pull Request - State: closed - Opened by lu000016 about 3 years ago

#37 - fix a typo in doc

Pull Request - State: closed - Opened by lu000016 about 3 years ago

#35 - some question about the paper

Issue - State: closed - Opened by ninjaxfy about 3 years ago - 1 comment

#35 - some question about the paper

Issue - State: closed - Opened by ninjaxfy about 3 years ago - 1 comment

#35 - some question about the paper

Issue - State: closed - Opened by ninjaxfy about 3 years ago - 1 comment

#34 - DEXSeq hangs

Issue - State: open - Opened by elenichri over 3 years ago

#34 - DEXSeq hangs

Issue - State: open - Opened by elenichri over 3 years ago

#34 - DEXSeq hangs

Issue - State: open - Opened by elenichri over 3 years ago

#33 - estimating promoter activity from given bam files

Issue - State: closed - Opened by ninjaxfy over 3 years ago - 4 comments

#33 - estimating promoter activity from given bam files

Issue - State: closed - Opened by ninjaxfy over 3 years ago - 4 comments

#33 - estimating promoter activity from given bam files

Issue - State: closed - Opened by ninjaxfy over 3 years ago - 4 comments

#32 - Docker image for proActiv

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

#32 - Docker image for proActiv

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

#32 - Docker image for proActiv

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

#31 - Not summarized values across conditions

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

#31 - Not summarized values across conditions

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

#31 - Not summarized values across conditions

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

#30 - invalid class "DESeqDataSet" object error

Issue - State: closed - Opened by elenichri over 3 years ago - 6 comments

#30 - invalid class "DESeqDataSet" object error

Issue - State: closed - Opened by elenichri over 3 years ago - 6 comments

#30 - invalid class "DESeqDataSet" object error

Issue - State: closed - Opened by elenichri over 3 years ago - 6 comments

#27 - map to txId by promoterId

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

#27 - map to txId by promoterId

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

#27 - map to txId by promoterId

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

#26 - getAlternativePromoters (Bioconductor version dont have it)

Issue - State: closed - Opened by ashokpatowary over 3 years ago - 1 comment

#26 - getAlternativePromoters (Bioconductor version dont have it)

Issue - State: closed - Opened by ashokpatowary over 3 years ago - 1 comment

#25 - preparePromoterAnnotation for different species

Issue - State: closed - Opened by gabee-chan almost 4 years ago - 5 comments

#25 - preparePromoterAnnotation for different species

Issue - State: closed - Opened by gabee-chan almost 4 years ago - 5 comments

#24 - update installation guide to Bioconductor

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

#24 - update installation guide to Bioconductor

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

#23 - getTranscriptRanges() function limits species this can be applied to

Issue - State: closed - Opened by G-Thomson over 4 years ago - 2 comments

#23 - getTranscriptRanges() function limits species this can be applied to

Issue - State: closed - Opened by G-Thomson over 4 years ago - 2 comments

#22 - No major promoter when internal promoters are strong

Issue - State: open - Opened by lukauskas over 4 years ago - 2 comments
Labels: question

#22 - No major promoter when internal promoters are strong

Issue - State: open - Opened by lukauskas over 4 years ago - 2 comments
Labels: question

#21 - Example of how to generate junction file from fastq

Issue - State: open - Opened by lukauskas over 4 years ago - 1 comment
Labels: enhancement