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

#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

#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

#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

#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

#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

#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

#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

#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

#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

#449 - Update README.md

Pull Request - State: closed - Opened by vyepez88 over 1 year ago

#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