Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / gagneurlab/drop issues and pull requests
#536 - Error in h(simpleError(msg, call))
Issue -
State: open - Opened by pkrithivasan 5 months ago
- 1 comment
#535 - Writing `rds` files as log can crash Snakemake execution
Issue -
State: open - Opened by votti 6 months ago
#534 - Incompatible with `Snakemake>=8`
Issue -
State: open - Opened by votti 6 months ago
- 1 comment
#533 - Adds space between `#+` and `echo`
Pull Request -
State: closed - Opened by votti 6 months ago
#532 - Chunk options `#+echo` not correctly parsed
Issue -
State: open - Opened by votti 6 months ago
- 1 comment
#529 - Default running folder is out of space
Issue -
State: closed - Opened by hermean 6 months ago
- 2 comments
#528 - CalledProcessError in installRPackages.R
Issue -
State: open - Opened by gaynora7 6 months ago
- 4 comments
#527 - Error in MAE QC create matrix dna rna cor
Issue -
State: closed - Opened by bijuissac 6 months ago
- 3 comments
#526 - Error in AberrantSplicing_pipeline_FRASER_04_fit_hyperparameters_FraseR_R
Issue -
State: closed - Opened by pkrithivasan 6 months ago
- 3 comments
#525 - Error running aberrantSplicing
Issue -
State: closed - Opened by pkrithivasan 7 months ago
- 2 comments
#524 - lymphoblastoid cell lines datasets of gene counts
Issue -
State: closed - Opened by Matteo1988 7 months ago
#523 - Running pipeline offline in trusted research environemnt
Issue -
State: open - Opened by chrisodhams 7 months ago
- 1 comment
#521 - Is there a way to specify sample and controls in runs?
Issue -
State: closed - Opened by dissakov 8 months ago
- 10 comments
#520 - Does FRASER make any comparisons between genes, or only comparing splicing within a given gene (between sample and controls)?
Issue -
State: open - Opened by dissakov 8 months ago
- 1 comment
#519 - OOM error in markDuplicates
Issue -
State: closed - Opened by gianfilippo 8 months ago
- 3 comments
#518 - error in mae
Issue -
State: open - Opened by Acetyl-ZHOU 8 months ago
- 8 comments
#517 - Aberrant splicing theta (θ) values width all have the same value
Issue -
State: closed - Opened by carlalbc 8 months ago
- 2 comments
#516 - error in aberrantExpression module
Issue -
State: closed - Opened by jfertaj 8 months ago
- 2 comments
#515 - TypeError in file /DATA/drop_demo/Snakefile, line 12: expected str, bytes or os.PathLike object, not NoneType
Issue -
State: open - Opened by Acetyl-ZHOU 8 months ago
- 1 comment
#514 - Aberrant Splicing: error in 01_1_countRNA_splitReads_samplewise.R, [,j] index out of bounds
Issue -
State: closed - Opened by kdewispelaere 8 months ago
- 1 comment
#513 - QC variants are all homozygous causing MAE rule MonoallelicExpression_pipeline_QC_deseq_qc_R to error out
Issue -
State: closed - Opened by wanqingshao 8 months ago
- 1 comment
#512 - Pipeline runs as expected, but results folder is blank?
Issue -
State: closed - Opened by dissakov 8 months ago
- 1 comment
#511 - One sample + external data vs multiple samples + external data
Issue -
State: closed - Opened by gianfilippo 8 months ago
- 15 comments
#510 - DROP installation issue on linux cluster
Issue -
State: open - Opened by gianfilippo 8 months ago
- 1 comment
Labels: enhancement
#509 - ImportError: cannot import name 'get_argument_parser' from 'snakemake'
Issue -
State: closed - Opened by TechLabLgm 9 months ago
- 3 comments
#508 - Annotating results with Ensembl Id or HGNC Id
Issue -
State: open - Opened by Lucpen 9 months ago
- 2 comments
#507 - AberrantSplicing pipeline error
Issue -
State: open - Opened by akhilvelluva 9 months ago
- 4 comments
#506 - micromamba snakemake import error
Issue -
State: closed - Opened by akhilvelluva 9 months ago
- 2 comments
#505 - ImportError: cannot import name 'get_argument_parser' from 'snakemake'
Issue -
State: open - Opened by sgomes-catarina 9 months ago
- 2 comments
#504 - BiocParallel errors in rule AberrantExpression_pipeline_OUTRIDER_runOutrider_R
Issue -
State: closed - Opened by gianfilippo 10 months ago
- 7 comments
#503 - Results of original DROP publication
Issue -
State: closed - Opened by AEstebanMar 10 months ago
- 8 comments
#502 - demo failig
Issue -
State: closed - Opened by gianfilippo 10 months ago
- 1 comment
#501 - Unexpected results for RNA-DNA Matching
Issue -
State: closed - Opened by arual97 10 months ago
- 4 comments
#500 - Using long and short reads in the aberrant splicing analysis.
Issue -
State: closed - Opened by SergeyBioinformatics 10 months ago
- 1 comment
#499 - Differences between FRASER1 and FRASER2
Issue -
State: closed - Opened by dissakov 10 months ago
- 3 comments
#498 - Rerun Triggers of DROP
Issue -
State: closed - Opened by mincej 11 months ago
- 2 comments
#497 - How to specify the correction of autoencoder
Issue -
State: closed - Opened by kendaida 11 months ago
- 2 comments
#496 - Error with installing outrider and fraser on M1 Mac
Issue -
State: open - Opened by HMorsy 11 months ago
#495 - Building plots with abberant splicing results
Issue -
State: open - Opened by SergeyBioinformatics 11 months ago
- 4 comments
#494 - MissingInputException: Missing input files for rule mae_allelicCounts:
Issue -
State: closed - Opened by lbundalian about 1 year ago
- 7 comments
#493 - Error in reducer$value.cache[[as.character(idx)]] <- values
Issue -
State: closed - Opened by ChiaraF32 about 1 year ago
- 8 comments
#492 - Error in rule AberrantSplicing_pipeline_Counting_00_define_datasets_from_anno_R
Issue -
State: closed - Opened by frankaugs about 1 year ago
- 3 comments
#491 - Missed call - not clear why
Issue -
State: open - Opened by gevro about 1 year ago
- 2 comments
#490 - drop demo not working: Error in find_NCBI_assembly_ftp_dir
Issue -
State: closed - Opened by SamuelNicaise about 1 year ago
- 5 comments
#489 - DROP_1.3.3.yaml package update required?
Issue -
State: open - Opened by chrisodhams about 1 year ago
- 7 comments
#488 - Is it possible to use drop without snakemake?
Issue -
State: closed - Opened by geocarvalho about 1 year ago
- 1 comment
#487 - Using external count in FRASER2?
Issue -
State: closed - Opened by thudaniel2333 about 1 year ago
- 5 comments
#486 - Error in AberrantSplicing_pipeline_FRASER_08_extract_results_FraseR_R
Issue -
State: open - Opened by wanqingshao about 1 year ago
- 30 comments
#485 - Error in bamFile(fds[, samples(fds) == sampleID])[[1]]
Issue -
State: closed - Opened by dissakova about 1 year ago
- 1 comment
#484 - Error in rule AberrantSplicing_pipeline_FRASER_Summary_R:
Issue -
State: closed - Opened by dissakova about 1 year ago
- 3 comments
#483 - Error in FRASER_Summary_R
Issue -
State: closed - Opened by muhligs about 1 year ago
- 4 comments
#482 - No paired-end reads were detected in paired-end read library
Issue -
State: closed - Opened by dissakova about 1 year ago
- 9 comments
#481 - Softlink
Pull Request -
State: closed - Opened by nickhsmith about 1 year ago
#480 - Error in rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R:
Issue -
State: closed - Opened by dissakova over 1 year ago
- 10 comments
#479 - Error in rule changeHeader
Issue -
State: closed - Opened by muhligs over 1 year ago
- 7 comments
#478 - Error in rule MonoallelicExpression_pipeline_QC_create_matrix_dna_rna_cor_R:
Issue -
State: closed - Opened by dfermin over 1 year ago
- 4 comments
#477 - drop demo fails at rnaVariantCalling/pipeline/Snakefile line 446
Issue -
State: open - Opened by nicholas-owen over 1 year ago
- 18 comments
#476 - Estimated run-time for FRASER2
Issue -
State: open - Opened by chrisodhams over 1 year ago
- 13 comments
#475 - no suitable codecs found
Issue -
State: closed - Opened by ChiaraF32 over 1 year ago
- 1 comment
#474 - Error in merge.data.table() - AberrantExpression_pipeline_OUTRIDER_pvalsOutrider_R
Issue -
State: open - Opened by canankolakoglu over 1 year ago
- 3 comments
#473 - Drop 1.3.3 error in AberrantSplicing_pipeline_FRASER_04_fit_hyperparameters_FraseR_R
Issue -
State: closed - Opened by muhligs over 1 year ago
- 30 comments
#472 - Split read recount should actually do a recount
Issue -
State: closed - Opened by aerval over 1 year ago
- 4 comments
#471 - Error in model.matrix.default(Terms, m) : variable 1 has no levels
Issue -
State: closed - Opened by ChiaraF32 over 1 year ago
- 3 comments
#470 - Are there plans to produce a dockerfile for DROP
Issue -
State: closed - Opened by PeterKneale over 1 year ago
- 1 comment
#469 - AberrantSplicing error in DROP version 1.3.3
Issue -
State: closed - Opened by jukerbox over 1 year ago
- 6 comments
#468 - DESeq dataset error thrown with aberrantExpression module
Issue -
State: closed - Opened by gaynora7 over 1 year ago
- 15 comments
#467 - AberrantSplicing error of drop1.2.4
Issue -
State: closed - Opened by liffcardio over 1 year ago
- 11 comments
#466 - oo few IDs in DROP_GROUP mae, please ensure that it has at least 1 IDs, groups: []
Issue -
State: open - Opened by SpaceCropTechnologies over 1 year ago
- 18 comments
#465 - Information on filtered genes
Issue -
State: closed - Opened by mincej over 1 year ago
- 3 comments
#464 - fix result script in case of no significant results
Pull Request -
State: open - Opened by ischeller over 1 year ago
#463 - Pipeline stops if group returns no results - FRASER2
Issue -
State: closed - Opened by mincej over 1 year ago
- 2 comments
#462 - Workflow error
Issue -
State: open - Opened by oliviatoles over 1 year ago
- 5 comments
#461 - AE error running single sample with external counts
Issue -
State: closed - Opened by muhligs over 1 year ago
- 6 comments
#459 - Running with single sample and external counts
Issue -
State: closed - Opened by muhligs over 1 year ago
- 2 comments
#458 - Error in if (cfg$aberrantSplicing$FRASER_version == "FRASER2")
Issue -
State: closed - Opened by ChiaraF32 over 1 year ago
- 2 comments
#457 - Support for multiple configurations?
Issue -
State: closed - Opened by mincej over 1 year ago
- 3 comments
#456 - Unable to create environment due to 'bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0'
Issue -
State: closed - Opened by dfermin over 1 year ago
- 2 comments
#455 - The drop command cannot be executed in an environment built with drop_1_3_3.ymal
Issue -
State: closed - Opened by liffcardio over 1 year ago
- 7 comments
#454 - Error in rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
Issue -
State: open - Opened by chrisodhams over 1 year ago
- 6 comments
#453 - 1.3.3
Pull Request -
State: closed - Opened by ischeller over 1 year ago
#452 - Splice analysis using external data cannot be merged with local files
Issue -
State: open - Opened by zshu-alt over 1 year ago
- 1 comment
#451 - rnaVariantCalling - All reads filtered by MappingQualityNotZeroReadFilter
Issue -
State: open - Opened by mincej over 1 year ago
- 2 comments
#450 - DROP 1.3.1 - Error in rule AberrantSplicing_pipeline_FRASER_08_extract_results_FraseR_R
Issue -
State: closed - Opened by mincej over 1 year ago
- 13 comments
#449 - Update README.md
Pull Request -
State: closed - Opened by vyepez88 over 1 year ago
#446 - MissingOutputException in rule AberrantSplicing_pipeline_Counting_01_2_countRNA_splitReads_merge_R
Issue -
State: closed - Opened by mincej over 1 year ago
- 14 comments
#438 - Usage on one sample vs many samples
Issue -
State: closed - Opened by mincej over 1 year ago
- 6 comments
#437 - Error in AS and export counts with external kidney cortex data
Issue -
State: closed - Opened by agomez700 over 1 year ago
- 1 comment
#435 - An error in MonoallelicExpression_pipeline_MAE_deseq_mae_R
Issue -
State: closed - Opened by ym-chen over 1 year ago
- 5 comments
#432 - FRASER Resources and Run Time
Issue -
State: closed - Opened by lemdcock over 1 year ago
- 1 comment
#431 - FRASER Error in check_returned_array
Issue -
State: closed - Opened by lemdcock over 1 year ago
- 3 comments
#428 - dataset too big?
Issue -
State: closed - Opened by AnikoSabo over 1 year ago
- 7 comments
#427 - drop demo fails in leftNormalVCF step
Issue -
State: open - Opened by dplassard over 1 year ago
- 3 comments
Labels: enhancement
#425 - Missing input files at dry-run
Issue -
State: open - Opened by nacasfer over 1 year ago
- 13 comments
#424 - Help with external counts in sample sheet
Issue -
State: open - Opened by phillip-richmond-alamya over 1 year ago
- 4 comments
#423 - Error in rule AberrantExpression_pipeline_OUTRIDER_runOutrider_R:
Issue -
State: closed - Opened by noorsmal over 1 year ago
- 3 comments
#404 - Error in `[.data.table`(gtf_dt, , `:=`(N, 1:.N), by = gene_name)
Issue -
State: closed - Opened by JieHe233 almost 2 years ago
- 7 comments
#399 - Splicing: too many outliers reported
Issue -
State: closed - Opened by SathyaDarmalinggam almost 2 years ago
- 2 comments
#382 - Drop demo fails
Issue -
State: closed - Opened by arvindsundaram almost 2 years ago
- 13 comments
#285 - Different AE AS results
Issue -
State: open - Opened by Ennaim1 over 2 years ago
- 2 comments
#260 - ImportError: cannot import name 'SNAKEFILE_CHOICES' from 'snakemake'
Issue -
State: closed - Opened by aojielian almost 3 years ago
- 5 comments