Ecosyste.ms: Issues

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GitHub / LRGASP/lrgasp-submissions issues and pull requests

#48 - show have a pipeline name as well as submitter name

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

#47 - reference_transcript_id attribute not validated

Issue - State: open - Opened by diekhans almost 3 years ago
Labels: future

#46 - additional challenge 2 submission

Issue - State: open - Opened by mei-du almost 3 years ago - 2 comments

#45 - Challenge 3, long_short, Illumina + ONT dRNA submission

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

#44 - Comma-separated column names do not match libraries in experiment.json

Issue - State: closed - Opened by andrewprzh almost 3 years ago - 2 comments

#42 - mismatch between data matrix and synapse for simulated data id

Issue - State: open - Opened by diekhans almost 3 years ago

#41 - Unspecified parameter in model description

Issue - State: open - Opened by andrewprzh about 3 years ago

#40 - fix simulation tool mixup

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

#39 - conflicting info on simulated data sample identifiers

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

#38 - simulation software mixup

Issue - State: open - Opened by julienlag about 3 years ago - 1 comment

#37 - creating a team in Synapse is mandatory

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

#36 - lrgasp-validate-entry looks for non-gz files

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

#35 - lrgasp-tools ambiguous output

Issue - State: open - Opened by julienlag about 3 years ago - 1 comment

#34 - python virtual environment for submission/validation tools

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

#33 - unused reads in read-to-model map file format

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

#32 - Modify entries orgnaization to better match challenges

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

#31 - Synapse submitssion tools and documentation

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

#30 - add new Sequel II subread BAMs to the RNA-Seq data matrix

Issue - State: closed - Opened by julienlag about 3 years ago - 2 comments

#29 - document required login for synypse

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

#28 - PB adapters

Issue - State: closed - Opened by Lutri22 over 3 years ago - 2 comments

#27 - Simulation metadata

Pull Request - State: closed - Opened by andrewprzh over 3 years ago

#26 - minor changes in challenge description

Pull Request - State: closed - Opened by andrewprzh over 3 years ago

#25 - description for simulated data

Pull Request - State: closed - Opened by andrewprzh over 3 years ago

#24 - add aligner and parameters to metadata

Issue - State: closed - Opened by diekhans about 4 years ago - 1 comment

#23 - duplicate ids in different genes

Issue - State: closed - Opened by diekhans about 4 years ago - 2 comments

#22 - submission with IDs that do not match GTF

Issue - State: closed - Opened by diekhans about 4 years ago - 2 comments

#21 - Extra tab in one submitter

Issue - State: closed - Opened by diekhans about 4 years ago - 2 comments

#20 - ID column must be called “ID”, not IDs, nor transcript_id ...

Issue - State: closed - Opened by diekhans about 4 years ago - 2 comments

#18 - valid Python-style identifier

Issue - State: closed - Opened by julienlag about 4 years ago - 1 comment

#17 - Gene vs. transcript level expression

Issue - State: open - Opened by fairliereese over 4 years ago - 2 comments

#16 - consistency of transcript_id's in model GTF vs expression matrix

Issue - State: closed - Opened by julienlag over 4 years ago - 1 comment

#15 - File format conversion scripts for output from specific tools

Issue - State: open - Opened by fairliereese over 4 years ago - 1 comment

#14 - Do we need a separate JSON for the read to model map?

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

#13 - fix link to submission.json example

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

#12 - The Illumina GM12878 pilot data ENCSR000AEH does not include SIRVs

Issue - State: open - Opened by julienlag over 4 years ago - 3 comments

#11 - read id to model format

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

#10 - The challenge_id json property is misspelled

Issue - State: closed - Opened by julienlag over 4 years ago - 1 comment

#9 - The submission.json example is 404

Issue - State: closed - Opened by julienlag over 4 years ago - 1 comment

#8 - provide flowcell and kit version for ONT datasets

Issue - State: open - Opened by julienlag over 4 years ago - 1 comment

#7 - fixed links to model-format.md

Pull Request - State: closed - Opened by andrewprzh over 4 years ago - 1 comment

#6 - Define process for transfering files, recommend tools.

Issue - State: closed - Opened by diekhans over 4 years ago - 5 comments

#5 - Create Mapping_reads2transcript_format.md

Pull Request - State: closed - Opened by FJPardoPalacios over 4 years ago - 1 comment

#4 - Create expression_matrix_format.md

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

#3 - Added file format sections and submission sections

Pull Request - State: closed - Opened by anbrooks over 4 years ago - 1 comment

#2 - added illumina and pacbio fastq links to readme

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

#1 - Added table for GM12878 pilot data

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