ArnaudDroitLab/metagene2 issues and pull requests

#39 - Normalize BAM coverages by total reads within each sample

Issue - State: open - Opened by aliciagallego 10 months ago - 3 comments

#38 - Select specific BAM files and regions for plotting

Issue - State: open - Opened by aliciagallego 10 months ago

#37 - Outliers removal

Issue - State: open - Opened by aliciagallego 10 months ago - 2 comments

#36 - Coverage and normalization

Issue - State: open - Opened by aliciagallego 10 months ago - 1 comment

#35 - How to add TSS and TES on metagene plots for RIP-seq data?

Issue - State: open - Opened by MolyWang 11 months ago - 3 comments

#34 - error when set padding_size

Issue - State: open - Opened by yuhongning almost 3 years ago - 3 comments

#33 - mg$produce_metagene design and syntax for

Issue - State: open - Opened by bumproo over 3 years ago - 2 comments

#32 - metagene2: DESeq dependency?

Issue - State: closed - Opened by jvanbelzen over 3 years ago - 5 comments

#31 - Failing on Bioconductor builders

Issue - State: closed - Opened by lshep almost 4 years ago - 4 comments

#30 - Bioconductor: Maintainer email

Issue - State: closed - Opened by CharlesJB almost 4 years ago - 1 comment
Labels: documentation

#29 - Error while plotting metagene plot

Issue - State: closed - Opened by anksi over 4 years ago - 14 comments

#28 - Issues in producing Metagene plot

Issue - State: closed - Opened by chrmarinaccio almost 5 years ago - 11 comments

#27 - Cannot set design=NULL from produce_metagene

Issue - State: open - Opened by ericfournier2 almost 5 years ago
Labels: bug, enhancement

#26 - sample_count=0 causes error

Issue - State: closed - Opened by ericfournier2 almost 5 years ago

#25 - Cannot group bam files for all transcripts

Issue - State: closed - Opened by kaltinel almost 5 years ago - 6 comments

#24 - bin_coverages mixes up regions if they overlap

Issue - State: closed - Opened by ericfournier2 about 5 years ago
Labels: bug

#23 - Min bin_count error message has a typo

Issue - State: closed - Opened by ericfournier2 about 5 years ago
Labels: bug

#22 - BAM existence is checked even when they are not needed

Issue - State: open - Opened by ericfournier2 about 5 years ago
Labels: bug, enhancement

#21 - Improve documentation on control sample in reference and vignette

Issue - State: closed - Opened by twoshoes over 5 years ago - 3 comments
Labels: documentation

#20 - Normalization using own parameters

Issue - State: closed - Opened by ymkng over 5 years ago - 2 comments

#19 - Question about faceting

Issue - State: closed - Opened by ymkng over 5 years ago - 2 comments

#18 - parameter_manager should roll back to the last state if validation fails

Issue - State: closed - Opened by ericfournier2 over 5 years ago
Labels: enhancement

#17 - Add a validation on split_by value

Issue - State: closed - Opened by ericfournier2 over 5 years ago
Labels: enhancement

#16 - Add procedure for retrieving promoters to vignette

Issue - State: closed - Opened by ericfournier2 over 5 years ago - 1 comment
Labels: enhancement

#15 - Find a way to make paths in vignette more readable.

Issue - State: open - Opened by ericfournier2 over 5 years ago
Labels: enhancement, documentation

#14 - Add documentation to produce_metagene in vignette

Issue - State: closed - Opened by ericfournier2 over 5 years ago - 1 comment
Labels: bug

#13 - Add paragraph about differences with metagene1

Issue - State: closed - Opened by ericfournier2 over 5 years ago
Labels: enhancement

#12 - Explicitly disallow extend_reads and paired_end to both be specified at the same time.

Issue - State: closed - Opened by ericfournier2 over 5 years ago
Labels: enhancement

#11 - Add explicit error for when bin_count is larger than certain width(region)

Issue - State: closed - Opened by ericfournier2 over 5 years ago
Labels: enhancement

#10 - extend_read should not shrink genes.

Issue - State: open - Opened by ericfournier2 over 5 years ago - 2 comments
Labels: bug

#9 - strand_specific causes crash if one strand has no regions

Issue - State: closed - Opened by ericfournier2 over 5 years ago
Labels: bug

#8 - Add check making sure extend_reads is an integer value

Issue - State: closed - Opened by ericfournier2 over 5 years ago
Labels: enhancement

#7 - Different bam_files order generate different results

Issue - State: closed - Opened by ericfournier2 about 6 years ago
Labels: bug

#6 - When extend_read > 0, coverage regions must also be extended

Issue - State: closed - Opened by ericfournier2 about 6 years ago - 2 comments
Labels: bug

#5 - metagene2 does not deal with stranded regions correctly

Issue - State: closed - Opened by ericfournier2 about 6 years ago
Labels: bug

#4 - Normalization of merged bams produce wrong results

Issue - State: closed - Opened by ericfournier2 about 6 years ago
Labels: bug

#3 - Allow replacing the cores parameter

Issue - State: closed - Opened by ericfournier2 about 6 years ago - 1 comment
Labels: enhancement

#2 - NaN in binned coverage when bin_count > width(region)

Issue - State: closed - Opened by ericfournier2 about 6 years ago - 1 comment
Labels: bug

#1 - Move coverage management to bam_handler

Issue - State: open - Opened by ericfournier2 about 6 years ago
Labels: enhancement

GitHub / ArnaudDroitLab/metagene2 issues and pull requests