csoneson/ARMOR issues and pull requests

#119 - Update conda install in GHA

Pull Request - State: closed - Opened by csoneson 5 months ago

#118 - Update R to v 4.4.1

Pull Request - State: closed - Opened by csoneson 5 months ago

#117 - Add MASS and Matrix to R environment

Pull Request - State: closed - Opened by csoneson 7 months ago

#100 - Error running example files

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

#99 - trouble running the pipeline for a bacterial species

Issue - State: closed - Opened by anzezupanic over 4 years ago - 13 comments

#98 - Specify channel in environment_R.yaml

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

#97 - Error when using bacterial fa and gtf file in ARMOR

Issue - State: closed - Opened by luongphekidz07 over 4 years ago - 26 comments

#96 - R4.0

Pull Request - State: closed - Opened by csoneson almost 5 years ago

#95 - Actions

Pull Request - State: closed - Opened by csoneson about 5 years ago

#94 - trouble with running the example dataset

Issue - State: closed - Opened by anzezupanic about 5 years ago - 4 comments

#93 - Fix empty check

Pull Request - State: closed - Opened by csoneson over 5 years ago

#92 - Gencode / Ensembl

Issue - State: closed - Opened by ms-gx over 5 years ago - 5 comments

#91 - Travis runtime

Pull Request - State: closed - Opened by khembach over 5 years ago

#90 - Fix msigdbr() function call in edgeR_dge.Rmd

Pull Request - State: closed - Opened by khembach over 5 years ago

#89 - Error when running the example dataset

Issue - State: closed - Opened by ms-gx over 5 years ago - 7 comments

#88 - About threads/cores

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

#87 - Tximport fix

Pull Request - State: closed - Opened by sorjuela over 5 years ago

#86 - Benchmarks

Pull Request - State: closed - Opened by csoneson almost 6 years ago

#85 - error in rule bigwig

Issue - State: closed - Opened by rrdavis77 almost 6 years ago - 4 comments

#84 - add sticker

Pull Request - State: closed - Opened by sorjuela almost 6 years ago

#83 - tximeta error

Issue - State: closed - Opened by ruqianl almost 6 years ago - 1 comment

#82 - Read csv

Pull Request - State: closed - Opened by csoneson almost 6 years ago

#81 - New commit breaks conda activation?

Issue - State: closed - Opened by devang-mehta almost 6 years ago - 12 comments

#80 - add multicore (via `ncores:`) to pkginstall/DRIMSeq rules

Pull Request - State: closed - Opened by markrobinsonuzh almost 6 years ago

#79 - Input exception wit SE reads

Issue - State: closed - Opened by devang-mehta almost 6 years ago - 10 comments

#78 - CalledProcessError in EdgeR

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

#77 - Add ARMOR version info

Pull Request - State: closed - Opened by csoneson almost 6 years ago

#76 - `Ncpu` in `install.packages()` ?

Issue - State: closed - Opened by markrobinsonuzh almost 6 years ago - 1 comment

#75 - Add multi-core into the R part?

Issue - State: closed - Opened by markrobinsonuzh almost 6 years ago - 1 comment

#74 - Extend checkinputs

Pull Request - State: closed - Opened by fionarhuang almost 6 years ago

#73 - extend the checkinputs to check all inputs

Issue - State: closed - Opened by fionarhuang almost 6 years ago - 2 comments

#72 - Update sce

Pull Request - State: closed - Opened by fionarhuang almost 6 years ago

#71 - Smallfixes

Pull Request - State: closed - Opened by csoneson almost 6 years ago

#70 - Check design contrast

Pull Request - State: closed - Opened by fionarhuang almost 6 years ago

#69 - Changes to SCEs

Issue - State: closed - Opened by csoneson almost 6 years ago

#68 - Runmodes diagram

Pull Request - State: closed - Opened by khembach almost 6 years ago

#67 - Camera optional

Pull Request - State: closed - Opened by csoneson almost 6 years ago

#66 - clarify how paths in config.yaml need to be specified

Issue - State: closed - Opened by csoneson almost 6 years ago - 1 comment

#65 - Multi experiment

Pull Request - State: closed - Opened by markrobinsonuzh almost 6 years ago

#64 - extend checks of input variables

Issue - State: closed - Opened by csoneson almost 6 years ago - 1 comment

#63 - Clean up `multi_experiment` branch

Issue - State: closed - Opened by markrobinsonuzh almost 6 years ago - 1 comment

#62 - improve the code to have the group variable

Pull Request - State: closed - Opened by fionarhuang almost 6 years ago - 1 comment

#61 - Allow arbitrary suffixes for fastq files

Pull Request - State: closed - Opened by csoneson almost 6 years ago

#60 - Setuprule

Pull Request - State: closed - Opened by csoneson almost 6 years ago - 1 comment

#59 - `setup` rule

Issue - State: closed - Opened by csoneson almost 6 years ago - 1 comment

#58 - FASTQ file sample suffix

Issue - State: closed - Opened by csoneson almost 6 years ago - 2 comments

#57 - remove groupvar

Pull Request - State: closed - Opened by fionarhuang almost 6 years ago - 4 comments

#56 - groupvar

Issue - State: closed - Opened by csoneson almost 6 years ago - 4 comments

#55 - pandoc

Issue - State: closed - Opened by csoneson almost 6 years ago - 4 comments

#54 - Fix links in README

Pull Request - State: closed - Opened by csoneson about 6 years ago

#53 - Camera

Pull Request - State: closed - Opened by csoneson about 6 years ago

#52 - Move images to subdirectory.

Pull Request - State: closed - Opened by csoneson about 6 years ago

#51 - Rename existing Rmd file instead of breaking (if forceOverwrite=TRUE)

Pull Request - State: closed - Opened by csoneson about 6 years ago

#50 - Success message

Pull Request - State: closed - Opened by csoneson about 6 years ago

#49 - add texts to Rmd files

Pull Request - State: closed - Opened by fionarhuang about 6 years ago

#48 - Rename wiki pages with number to put them in the right order

Issue - State: closed - Opened by csoneson about 6 years ago - 1 comment

#47 - Vignette of public data set analysis

Issue - State: closed - Opened by csoneson about 6 years ago - 2 comments

#46 - extend DRIMSeq Rmd text

Issue - State: closed - Opened by csoneson about 6 years ago - 2 comments

#45 - Travis

Pull Request - State: closed - Opened by csoneson about 6 years ago

#44 - Diagram

Pull Request - State: closed - Opened by sorjuela about 6 years ago

#43 - - remove prepare_results_for_shiny.R

Pull Request - State: closed - Opened by fionarhuang about 6 years ago

#42 - Fix tximeta for gencode

Pull Request - State: closed - Opened by csoneson about 6 years ago

#41 - Add success/error messages in Snakefile

Issue - State: closed - Opened by csoneson about 6 years ago - 1 comment

#40 - consistent chunk names in Rmd files

Issue - State: closed - Opened by csoneson about 6 years ago - 1 comment

#39 - Rmarkdown

Pull Request - State: closed - Opened by csoneson about 6 years ago

#38 - Fix bigwig rule

Issue - State: closed - Opened by csoneson about 6 years ago - 1 comment

#37 - Add example data

Pull Request - State: closed - Opened by csoneson over 6 years ago

#36 - Add documentation about .Renviron file

Issue - State: closed - Opened by csoneson over 6 years ago - 1 comment

#35 - move example data into repo

Issue - State: closed - Opened by csoneson over 6 years ago - 1 comment

#34 - useCondaR variable

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

#33 - Make sure gitinstall rule runs first

Issue - State: closed - Opened by csoneson over 6 years ago - 1 comment

#32 - Sce update

Pull Request - State: closed - Opened by fionarhuang over 6 years ago

#31 - Make nice diagram of workflow for paper

Issue - State: closed - Opened by sorjuela over 6 years ago - 2 comments

#30 - Unit testing

Issue - State: closed - Opened by sorjuela over 6 years ago - 2 comments

#29 - Fix some typos and add some text to the config.yaml file

Pull Request - State: closed - Opened by csoneson over 6 years ago

#28 - Custom isee panels

Pull Request - State: closed - Opened by csoneson over 6 years ago

#27 - Update README with links to wiki pages

Pull Request - State: closed - Opened by csoneson over 6 years ago

#26 - Drimseq fixes

Pull Request - State: closed - Opened by sorjuela over 6 years ago

#25 - Set output dir

Pull Request - State: closed - Opened by csoneson over 6 years ago

#24 - Gitinstall rule stephany

Pull Request - State: closed - Opened by sorjuela over 6 years ago

#23 - Conda env rules

Pull Request - State: closed - Opened by csoneson over 6 years ago

#22 - input and output directories

Pull Request - State: closed - Opened by fionarhuang over 6 years ago - 1 comment

#21 - Software version numbers

Issue - State: closed - Opened by csoneson over 6 years ago - 2 comments

#20 - Stephany gencode edit

Pull Request - State: closed - Opened by sorjuela over 6 years ago - 1 comment

#19 - R packages not available from conda

Issue - State: closed - Opened by csoneson over 6 years ago - 8 comments

#18 - Complete description in Wiki (snakemake installation, any others?)

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

#17 - input and output directories

Issue - State: closed - Opened by csoneson over 6 years ago - 2 comments

#16 - add conda environment to individual rules

Issue - State: closed - Opened by csoneson over 6 years ago - 1 comment

#15 - Salmon bias

Pull Request - State: closed - Opened by csoneson over 6 years ago

#14 - Export SingleCellExperiment and SummarizedExperiment

Pull Request - State: closed - Opened by fionarhuang over 6 years ago - 4 comments

#13 - Convert statistical analysis scripts into R/markdown templates

Issue - State: closed - Opened by csoneson over 6 years ago - 4 comments

#12 - trying to get yaml that works cross-platform and without .condarc

Pull Request - State: closed - Opened by markrobinsonuzh over 6 years ago

#11 - Add 'camera' for gene set testing?

Issue - State: closed - Opened by markrobinsonuzh over 6 years ago - 4 comments

#10 - Make trimming optional

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

#9 - "Methods" document

Issue - State: closed - Opened by csoneson over 6 years ago - 1 comment

#8 - Docker?

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

#7 - provide example data

Issue - State: closed - Opened by csoneson over 6 years ago - 1 comment

#6 - Add bias parameters to Salmon call

Issue - State: closed - Opened by csoneson over 6 years ago - 1 comment

#5 - Test across operating systems

Issue - State: closed - Opened by csoneson over 6 years ago - 1 comment

#4 - Export `SummarizedExperiment` object

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

GitHub / csoneson/ARMOR issues and pull requests