Issues
- 0
Error during test execution
#50 opened by asilvestris84 - 8
network issue for jcmq.run
#49 opened by shengxindaniu - 3
ERROR: Could not find a version that satisfies the requirement tensorflow==2.3.0 (from snaf)
#47 opened by zachhiteng - 1
Should the sequencing depth of different datasets and batch effect issues be considered when merging RNA-seq data from different cohorts for input?
#48 opened by jsrgwqx - 7
When jcmq.run, error in subexon_tran
#33 opened by LIH-WHU - 0
How to run netMHCpan for millions of pHLA?
#46 opened by frankligy - 5
Creating meta file within SPRINT pipeline
#43 opened by UCSFJL - 1
- 4
No neoantigens table in #Interactive Neoantigen Viewer# (TypeError: 'NoneType' object is not subscriptable)
#44 opened by hywyh2018 - 6
- 5
How to generate the gtex_ctrl_db and tcga_matched_control_junction_count.h5ad, it is a good control.
#41 opened by renyuan001 - 3
- 2
library lxml not supported. WikiPathways and LineageProfiler visualization will not work. Please install with pip install lxml.
#39 opened by renyuan001 - 2
Making customized control
#34 opened by thestarocean - 6
Longer epitope sequences
#31 opened by p-levy - 0
- 0
- 0
Sorting combined GFF
#36 opened by nsalomonis - 0
How to construct custom GTF/GFF for SNAF-B?
#35 opened by frankligy - 8
None of ['query'] are in the columns
#32 opened by haoqing12 - 8
Memory Overflow Issue During SNAF Execution
#27 opened by yiolino - 1
Broken dependeny reqirements?
#29 opened by TheWizier - 1
No such file or directory "assets"
#30 opened by LucaMannino - 0
slight discrepancies of junction frequency between freq0 file and B antigen result
#28 opened by frankligy - 6
IOError: File /mnt/altanalyze_output/AltResults/AlternativeOutput/Hs_RNASeq_top_alt_junctions-PSI_EventAnnotation.txt does not exist
#23 opened by Emptyset110 - 3
Unable to install
#21 opened by iskandr - 3
Understanding output columns
#26 opened by spvensko - 1
- 4
snaf.JunctionCountMatrixQuery.generate_results: KeyError: "None of ['query'] are in the columns"
#25 opened by infWang - 0
add support for EST data as well
#5 opened by frankligy - 0
singularity running AltAnalyze bug
#13 opened by frankligy - 1
- 0
next release remember to update database
#12 opened by frankligy - 1
can you process gff2 instead of gtf
#16 opened by frankligy - 1
- 0
doc error for splicing differential analysis
#18 opened by frankligy - 0
- 0
Rare scenario where uniprot sequence is one amino acid different than Ensembl
#15 opened by frankligy - 0
- 1
in next docker image, install parallel
#8 opened by frankligy - 1
filtering out B antigen candidates where predicted peptides fully contained in reference
#11 opened by frankligy - 1
annotate the T antigen
#1 opened by frankligy - 0
add documents for newly added function
#10 opened by frankligy - 0
- 1
- 0
- 0
- 0
Steps to make this package
#4 opened by frankligy - 0