frankligy/SNAF issues and pull requests

#57 - Testing example failed?

Issue - State: open - Opened by malonzm1 9 days ago - 5 comments

#56 - Installation question

Issue - State: open - Opened by swbujnowski 15 days ago - 1 comment

#55 - cannot run the test sample (OSError: [Errno 12] Cannot allocate memory; multiprocessing)

Issue - State: open - Opened by cjhong 21 days ago - 1 comment

#54 - Program freezes when processing large input files

Issue - State: open - Opened by LIH-WHU 3 months ago - 1 comment

#53 - Error when setting trypsin as enzyme for maxquant

Issue - State: open - Opened by frankligy 3 months ago
Labels: bug, announcement

#52 - Issue with Algorithm Progress Bar Stuck at jcmq.run - Assistance Requested

Issue - State: open - Opened by dnc-github 3 months ago - 5 comments

#51 - Neo-junction Annotation Clarification

Issue - State: closed - Opened by yiolino 4 months ago - 2 comments

#50 - Error during test execution

Issue - State: closed - Opened by asilvestris84 5 months ago

#49 - network issue for jcmq.run

Issue - State: open - Opened by shengxindaniu 5 months ago - 8 comments

#47 - ERROR: Could not find a version that satisfies the requirement tensorflow==2.3.0 (from snaf)

Issue - State: open - Opened by zachhiteng 7 months ago - 3 comments

#46 - How to run netMHCpan for millions of pHLA?

Issue - State: open - Opened by frankligy 7 months ago
Labels: announcement

#45 - Retreiving nucleotide coding sequence and genomic origin for peptides

Issue - State: open - Opened by spvensko 8 months ago - 1 comment

#44 - No neoantigens table in #Interactive Neoantigen Viewer# (TypeError: 'NoneType' object is not subscriptable)

Issue - State: open - Opened by hywyh2018 8 months ago - 4 comments

#43 - Creating meta file within SPRINT pipeline

Issue - State: open - Opened by UCSFJL 8 months ago - 5 comments

#42 - KeyError: "None of ['query'] are in the columns"

Issue - State: closed - Opened by renyuan001 9 months ago - 6 comments

#41 - How to generate the gtex_ctrl_db and tcga_matched_control_junction_count.h5ad, it is a good control.

Issue - State: open - Opened by renyuan001 9 months ago - 5 comments

#40 - how to subset a normal control from gtex or tcga?

Issue - State: open - Opened by renyuan001 10 months ago - 3 comments

#39 - library lxml not supported. WikiPathways and LineageProfiler visualization will not work. Please install with pip install lxml.

Issue - State: closed - Opened by renyuan001 10 months ago - 2 comments

#38 - rm: cannot remove './TMHMM_*': No such file or directory

Issue - State: open - Opened by frankligy 11 months ago

#37 - How to turn off GTEx control and use my own custom control samples?

Issue - State: open - Opened by frankligy 11 months ago
Labels: announcement

#36 - Sorting combined GFF

Issue - State: open - Opened by nsalomonis 11 months ago

#35 - How to construct custom GTF/GFF for SNAF-B?

Issue - State: open - Opened by frankligy 11 months ago
Labels: announcement

#34 - Making customized control

Issue - State: open - Opened by thestarocean 11 months ago - 2 comments

#33 - When jcmq.run, error in subexon_tran

Issue - State: open - Opened by LIH-WHU 12 months ago - 8 comments

#32 - None of ['query'] are in the columns

Issue - State: closed - Opened by haoqing12 12 months ago - 8 comments

#31 - Longer epitope sequences

Issue - State: open - Opened by p-levy about 1 year ago - 6 comments

#30 - No such file or directory "assets"

Issue - State: open - Opened by LucaMannino about 1 year ago - 1 comment

#29 - Broken dependeny reqirements?

Issue - State: closed - Opened by TheWizier about 1 year ago - 1 comment

#28 - slight discrepancies of junction frequency between freq0 file and B antigen result

Issue - State: open - Opened by frankligy about 1 year ago
Labels: help wanted

#27 - Memory Overflow Issue During SNAF Execution

Issue - State: closed - Opened by yiolino about 1 year ago - 8 comments

#26 - Understanding output columns

Issue - State: open - Opened by spvensko about 1 year ago - 3 comments

#25 - snaf.JunctionCountMatrixQuery.generate_results: KeyError: "None of ['query'] are in the columns"

Issue - State: open - Opened by infWang about 1 year ago - 4 comments

#24 - Incompatibility Issue with mhcgnomes version in SNAF Pipeline

Pull Request - State: closed - Opened by yiolino about 1 year ago - 2 comments

#23 - IOError: File /mnt/altanalyze_output/AltResults/AlternativeOutput/Hs_RNASeq_top_alt_junctions-PSI_EventAnnotation.txt does not exist

Issue - State: closed - Opened by Emptyset110 about 1 year ago - 6 comments

#22 - implement new function to get full length isoform for NeoJunction

Issue - State: open - Opened by frankligy about 1 year ago - 1 comment
Labels: enhancement

#21 - Unable to install

Issue - State: closed - Opened by iskandr about 1 year ago - 3 comments

#20 - The recommended tools and parameters used to generate the RNAseq alignment BAM.

Issue - State: closed - Opened by YingYa about 1 year ago - 1 comment

#19 - HLA allele can be 3 digit, edge case for reformatting

Issue - State: closed - Opened by frankligy about 1 year ago
Labels: bug

#18 - doc error for splicing differential analysis

Issue - State: closed - Opened by frankligy about 1 year ago
Labels: documentation

#17 - Bruker .d base mqpar.xml file has fixed modifications

Issue - State: closed - Opened by frankligy over 1 year ago - 1 comment
Labels: bug

#16 - can you process gff2 instead of gtf

Issue - State: closed - Opened by frankligy about 2 years ago - 1 comment
Labels: enhancement

#15 - Rare scenario where uniprot sequence is one amino acid different than Ensembl

Issue - State: open - Opened by frankligy about 2 years ago
Labels: help wanted

#14 - Visualizing function drawing order when dealing with I2.2

Issue - State: open - Opened by frankligy about 2 years ago
Labels: bug

#13 - singularity running AltAnalyze bug

Issue - State: closed - Opened by frankligy over 2 years ago
Labels: help wanted

#12 - next release remember to update database

Issue - State: closed - Opened by frankligy over 2 years ago
Labels: enhancement

#11 - filtering out B antigen candidates where predicted peptides fully contained in reference

Issue - State: closed - Opened by frankligy over 2 years ago - 1 comment
Labels: feature request

#10 - add documents for newly added function

Issue - State: closed - Opened by frankligy over 2 years ago
Labels: documentation

#9 - How to run docker and singularity on typical HPC?

Issue - State: closed - Opened by frankligy almost 3 years ago

#8 - in next docker image, install parallel

Issue - State: closed - Opened by frankligy almost 3 years ago - 1 comment
Labels: feature request

#7 - singularity different file system plus permission error

Issue - State: closed - Opened by frankligy almost 3 years ago - 1 comment
Labels: bug

#6 - step1 AltAnalyze intron bed file version conflict

Issue - State: closed - Opened by frankligy almost 3 years ago
Labels: bug

#5 - add support for EST data as well

Issue - State: closed - Opened by frankligy almost 3 years ago
Labels: feature request

#4 - Steps to make this package

Issue - State: closed - Opened by frankligy almost 3 years ago

#3 - altanalyze docker automatically generate subset of junction count matrix

Issue - State: closed - Opened by frankligy almost 3 years ago
Labels: feature request

#2 - macOS known minor bug - SNAF-T viewer weblogo

Issue - State: open - Opened by frankligy almost 3 years ago
Labels: bug

#1 - annotate the T antigen

Issue - State: closed - Opened by frankligy almost 3 years ago - 1 comment
Labels: feature request

GitHub / frankligy/SNAF issues and pull requests