GitHub / mritchielab/FLAMES issues and pull requests
#60 - Could I use FLAMES with only long-read ScRNA-seq data?
Issue -
State: open - Opened by brilliantlee2 about 2 months ago
- 2 comments
#59 - Feature Request: Add genome_fa_mmi Support to SingleCellPipeline
Issue -
State: open - Opened by nci-tech about 2 months ago
- 1 comment
#58 - Reduce output file sizes in single-cell pipelines
Pull Request -
State: closed - Opened by chingyinwan 2 months ago
- 1 comment
#57 - Error with sparse matrix in sc_DTU_analysis function
Issue -
State: closed - Opened by MaveVu 3 months ago
- 1 comment
#56 - Sefi pull request - FLAMES Improved speed, clarity & config file
Pull Request -
State: closed - Opened by Sefi196 4 months ago
#55 - How to assign transcript to cell type?
Issue -
State: open - Opened by SziKayLeung 4 months ago
- 1 comment
#54 - Memory overflow during gene count matrix finalization
Issue -
State: open - Opened by nci-tech 4 months ago
- 2 comments
#53 - Missing packages during installation
Issue -
State: closed - Opened by jadedavis5 5 months ago
- 4 comments
#52 - Question about changing parameters for BLAZE in sc_long_pipeline
Issue -
State: closed - Opened by genome2020 6 months ago
- 2 comments
#51 - Gene-level counts from sc_long_pipeline
Issue -
State: closed - Opened by ghowitt 9 months ago
- 1 comment
#50 - do_gene_quantification fails in sc_long_pipeline
Issue -
State: closed - Opened by beeesal 9 months ago
- 11 comments
#49 - question regarding `bulk_long_pipeline`
Issue -
State: open - Opened by sparthib 10 months ago
- 1 comment
Labels: enhancement
#48 - passing bam files to `sc_long_multisample_pipeline`
Issue -
State: closed - Opened by sparthib 10 months ago
- 8 comments
#47 - Question about lacking of two python packages
Issue -
State: closed - Opened by FeiGao0717 10 months ago
- 3 comments
#46 - question on UMI deduplication step
Issue -
State: closed - Opened by sparthib 10 months ago
- 3 comments
#45 - update basilisk env: add minimap2, samtools
Pull Request -
State: closed - Opened by ChangqingW 10 months ago
#44 - clarification on Isoform quantification parameters and output
Issue -
State: closed - Opened by sparthib 10 months ago
- 3 comments
#43 - Defining custom parameters in the config file
Issue -
State: open - Opened by vsuppiyar 11 months ago
- 2 comments
Labels: bug
#42 - FLAMES path
Issue -
State: closed - Opened by vsuppiyar 11 months ago
- 4 comments
Labels: bug
#41 - Assigning reads to genes stuck with 3 genes left
Issue -
State: closed - Opened by ljwharbers about 1 year ago
- 1 comment
#40 - UMI usage in genotyping
Issue -
State: closed - Opened by maxim-h about 1 year ago
- 3 comments
#39 - Fix GFF parser for gencode
Pull Request -
State: closed - Opened by maxim-h about 1 year ago
- 1 comment
#38 - Integrate Bambu results for multiple samples
Issue -
State: open - Opened by koehlek99 about 1 year ago
- 2 comments
#37 - Error with reading gene annotation file
Issue -
State: closed - Opened by sparthib about 1 year ago
- 3 comments
#36 - Visualizations
Issue -
State: closed - Opened by vasikara17 about 1 year ago
- 3 comments
#35 - Error starting the FLAMES pipeline
Issue -
State: closed - Opened by vasikara17 about 1 year ago
- 8 comments
Labels: bug
#34 - blaze dependency
Issue -
State: open - Opened by nick-youngblut about 1 year ago
- 3 comments
#33 - find_isoform error
Issue -
State: open - Opened by nick-youngblut about 1 year ago
- 4 comments
#32 - Isoform category quantification
Issue -
State: closed - Opened by lscdanson about 1 year ago
- 4 comments
#31 - Error: _Map_base::at
Issue -
State: open - Opened by nick-youngblut over 1 year ago
- 10 comments
Labels: bug
#30 - FileNotFoundError: matched_reads.fastq
Issue -
State: open - Opened by nick-youngblut over 1 year ago
- 8 comments
Labels: bug
#29 - 'asBam' failed to open SAM/BAM file
Issue -
State: closed - Opened by nick-youngblut over 1 year ago
- 5 comments
#28 - Manually setting threads
Issue -
State: closed - Opened by nick-youngblut over 1 year ago
- 3 comments
Labels: documentation
#27 - no transcript id
Issue -
State: closed - Opened by nick-youngblut over 1 year ago
- 3 comments
#26 - Could not locate k8 and/or paftools.js in the minimap2 folder, they are required for converting annotation to bed12 files
Issue -
State: closed - Opened by nick-youngblut over 1 year ago
- 13 comments
Labels: bug
#25 - The makeTxDb*() functions have moved from GenomicFeatures to txdbmaker
Pull Request -
State: closed - Opened by hpages over 1 year ago
- 1 comment
#24 - quesetion about combinesce
Issue -
State: closed - Opened by yuanwsy over 1 year ago
- 5 comments
#23 - feature request: better samtools dependency handling
Issue -
State: closed - Opened by nick-youngblut over 1 year ago
- 1 comment
#22 - Update cutadapt.R to fix broken cutadapt syntax
Pull Request -
State: closed - Opened by felixradtke over 1 year ago
#21 - Error: with minimap2 alignment and samtools
Issue -
State: closed - Opened by drafzalsyed over 1 year ago
- 3 comments
#20 - Error in locating minimap2
Issue -
State: closed - Opened by sh0rt2l0ng over 1 year ago
- 5 comments
#19 - Include gene name in mutation calling output file
Issue -
State: closed - Opened by HenriettaHolze over 1 year ago
- 1 comment
#18 - not detecting .bai in directory
Issue -
State: closed - Opened by m-noonan over 1 year ago
- 2 comments
Labels: documentation, question
#17 - Update the vignette of `create_config` function
Issue -
State: closed - Opened by youyupei over 1 year ago
- 1 comment
Labels: documentation
#16 - use with ONT workflow?
Issue -
State: closed - Opened by m-noonan almost 2 years ago
- 22 comments
Labels: enhancement, question
#15 - Please update vignette
Issue -
State: closed - Opened by HenriettaHolze almost 2 years ago
- 2 comments
#14 - Set `StagedInstall: no` in `DESCRIPTION`
Issue -
State: closed - Opened by waddella almost 2 years ago
- 2 comments
#13 - Installation issue on Debian 11
Issue -
State: closed - Opened by HaraldWilhelmi almost 2 years ago
- 1 comment
#12 - C++ find_isoform with multithreading
Pull Request -
State: closed - Opened by OliverVoogd almost 2 years ago
- 1 comment
#11 - Running Multisample pipeline
Issue -
State: closed - Opened by mcortes-lopez over 2 years ago
- 1 comment
#10 - Mutation function
Issue -
State: closed - Opened by mcortes-lopez over 2 years ago
- 1 comment
#9 - creats_se_from_dict annotation isn't optional
Issue -
State: closed - Opened by brianFSM over 2 years ago
#8 - C++copy to fix git merge issue
Pull Request -
State: closed - Opened by OliverVoogd over 3 years ago
#7 - compilation fails on aarch64 / arm64
Issue -
State: closed - Opened by kevinushey over 3 years ago
- 5 comments
#6 - Update sc_mutations.R
Pull Request -
State: closed - Opened by LuyiTian almost 4 years ago
#5 - please fix DESCRIPTION
Issue -
State: closed - Opened by vjcitn over 4 years ago
- 1 comment
#4 - update document
Pull Request -
State: closed - Opened by LuyiTian over 4 years ago
#3 - update description
Pull Request -
State: closed - Opened by LuyiTian over 4 years ago
#2 - Building vignette during package installation failure
Issue -
State: closed - Opened by PeteHaitch over 4 years ago
- 1 comment
#1 - R CMD check fixes
Pull Request -
State: closed - Opened by OliverVoogd over 4 years ago