Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / hzi-bifo/RiboDetector issues and pull requests
#56 - Ribodetector unable to remove rRNA reads from Toxoplasma gondii scRNASeq SmartSeq2 data
Issue -
State: open - Opened by Rohit-Satyam 22 days ago
- 3 comments
#55 - An error occurred while executing the ribodetector_cpu command.
Issue -
State: open - Opened by kinako0130 about 2 months ago
- 5 comments
#54 - error after 14 hours of processing
Issue -
State: closed - Opened by tulikasriv26 5 months ago
- 3 comments
#53 - unexpected large proportion of rRNA reads detected by RiboDetector
Issue -
State: closed - Opened by Ivy-ops 5 months ago
- 13 comments
#52 - Log file/progress formatting for better readability
Issue -
State: open - Opened by mckellardw 9 months ago
- 2 comments
#51 - RiboDetector for barcoded libraries
Issue -
State: closed - Opened by mckellardw 9 months ago
- 2 comments
Labels: enhancement
#50 - Mouse data compatibility
Issue -
State: closed - Opened by mmiots9 11 months ago
- 2 comments
#49 - No classification at all for some data and classification for some
Issue -
State: closed - Opened by EorgeKit 11 months ago
- 6 comments
#48 - Read Length question
Issue -
State: closed - Opened by singhbhavya 11 months ago
- 1 comment
#47 - fix the issue caused by less random default socket addresses for multiprocessing.Manager()
Issue -
State: closed - Opened by dawnmy about 1 year ago
#46 - Address already in use
Issue -
State: closed - Opened by lucacozzuto about 1 year ago
- 5 comments
#45 - Classification of the rRNA removed seqeunces
Issue -
State: closed - Opened by LeoVincenzi about 1 year ago
- 3 comments
#44 - Tuple range error
Issue -
State: closed - Opened by mwylerCH about 1 year ago
- 3 comments
#43 - Can we apply this tool for custom reference sequences?
Issue -
State: closed - Opened by ssun1116 about 1 year ago
- 2 comments
#42 - ValueError:you are required to explicitly set the providers parameter when instantiating InferenceSession
Issue -
State: closed - Opened by Abelcanc3rhack3r over 1 year ago
- 1 comment
Labels: onnxruntime
#41 - Can we use Ribodetector for rRNA quantification in scRNASeq?
Issue -
State: closed - Opened by Rohit-Satyam over 1 year ago
- 1 comment
Labels: enhancement
#40 - RuntimeError: indices should be either on cpu or on the same device as the indexed tensor (cpu)
Issue -
State: closed - Opened by caldodge over 1 year ago
- 9 comments
Labels: pytorch
#39 - The proportion of ribosome reads calculated by ribodetector is not equal to the proportion of ribosome protein count in ReadsPerGene.out.tab generated by STAR
Issue -
State: closed - Opened by li1311139481 over 1 year ago
- 2 comments
#38 - Retrive the filtered out sequences
Issue -
State: closed - Opened by LeoVincenzi over 1 year ago
- 2 comments
#37 - RiboDetector is identifying reads generated from ChrX and ChrY as rRNA reads
Issue -
State: closed - Opened by rajanbit over 1 year ago
- 4 comments
#36 - [ERROR] Unable to run ribodetector on a remote server: No visible CUDA devices!
Issue -
State: closed - Opened by jwilliams648 over 1 year ago
- 1 comment
#35 - Change the log info, from detect_cpu to ribodetector_cpu
Issue -
State: closed - Opened by dawnmy over 1 year ago
#34 - RiboDetector is not working on GPU mode
Issue -
State: closed - Opened by Nirmal2310 over 1 year ago
- 4 comments
#33 - Ability to produce a log file that can be easily processed by MultiQC
Issue -
State: closed - Opened by Rohit-Satyam almost 2 years ago
- 18 comments
Labels: bug, documentation, enhancement
#32 - Please use detect_cpu.py to run it on CPU if you do not have GPU or you need to install GPU version of PyTorch
Issue -
State: closed - Opened by Rohit-Satyam almost 2 years ago
- 2 comments
#31 - ribodetector_cpu hangs with SLURM
Issue -
State: closed - Opened by gianfilippo almost 2 years ago
- 4 comments
#30 - Recommendations on running RiboDetector twice on the fastq files?
Issue -
State: closed - Opened by resol341 almost 2 years ago
- 2 comments
#29 - ribodetector_cpu classifies and outputs more reads in the end than there were in the input data to begin with
Issue -
State: closed - Opened by erzakiev almost 2 years ago
- 13 comments
Labels: MacOS
#28 - Which organism?
Issue -
State: closed - Opened by Homap over 2 years ago
- 1 comment
#27 - Chunk size question
Issue -
State: closed - Opened by caity-s over 2 years ago
- 3 comments
#26 - gzip is very slow
Issue -
State: closed - Opened by alienzj over 2 years ago
- 1 comment
#25 - Question
Issue -
State: closed - Opened by deoliveira86 over 2 years ago
- 2 comments
#24 - Using RiboDetector on assembled contigs?
Issue -
State: closed - Opened by natashagriffin over 2 years ago
- 2 comments
#23 - question regarding confidence of -e norrna option
Issue -
State: closed - Opened by caity-s over 2 years ago
- 4 comments
#22 - docker image for 0.2.6
Issue -
State: closed - Opened by NicoleGruenheit over 2 years ago
- 3 comments
Labels: docker
#21 - False postivies when using on metagenomic data?
Issue -
State: closed - Opened by rezenman over 2 years ago
- 6 comments
#20 - About read length
Issue -
State: closed - Opened by gouwei1 over 2 years ago
- 2 comments
#19 - Is it possible using Ribodector on metagenomic reads
Issue -
State: closed - Opened by lideyongJNU over 2 years ago
- 1 comment
#18 - CPU mode hangs with macOS
Issue -
State: closed - Opened by omicz over 2 years ago
- 6 comments
Labels: onnxruntime, MacOS
#17 - cpu vs. gpu performance
Issue -
State: closed - Opened by ARW-UBT over 2 years ago
- 4 comments
#16 - read length should be not smaller than 50, but ribo-seq reads are ~30 bp
Issue -
State: closed - Opened by huguanjing over 2 years ago
- 4 comments
Labels: enhancement, question
#15 - Installation error in conda environemnt
Issue -
State: closed - Opened by ARW-UBT over 2 years ago
- 6 comments
#14 - Add model eval?
Issue -
State: closed - Opened by dawnmy over 2 years ago
- 1 comment
#13 - In CPU mode, smaller chunk_size does not reduce the memory use.
Issue -
State: closed - Opened by dawnmy almost 3 years ago
- 3 comments
Labels: enhancement
#12 - Memory Calculation Doubts
Issue -
State: closed - Opened by magcurly almost 3 years ago
- 7 comments
#11 - no rRNA sequences were detected in an almost complete genome
Issue -
State: closed - Opened by ThomasYJK555 almost 3 years ago
- 2 comments
#10 - Add chunk size support for loading the sequences to reduce memory use for large files
Issue -
State: closed - Opened by dawnmy almost 3 years ago
- 2 comments
Labels: enhancement
#9 - Memory issues with RiboDetector
Issue -
State: closed - Opened by akrinos almost 3 years ago
- 23 comments
Labels: bug, enhancement, onnxruntime, SLURM
#8 - GPU with higher CUDA version can not be used within old pytorch
Issue -
State: closed - Opened by sixvable almost 3 years ago
- 12 comments
#7 - Lost reads?
Issue -
State: closed - Opened by sjaenick almost 3 years ago
- 2 comments
#6 - Process hangs in CPU detection step
Issue -
State: closed - Opened by sjaenick almost 3 years ago
- 23 comments
Labels: bug, question, onnxruntime, SLURM
#5 - Optimize for CPU which supports AVX2 instruction
Issue -
State: open - Opened by dawnmy about 3 years ago
Labels: enhancement
#4 - Training for next main release
Issue -
State: closed - Opened by dawnmy about 3 years ago
#3 - Add tests
Issue -
State: open - Opened by dawnmy about 3 years ago
Labels: documentation
#2 - Train for long reads e.g. nanopore, pacbio
Issue -
State: open - Opened by dawnmy over 3 years ago
- 6 comments
Labels: enhancement
#1 - Add previous high divergent rRNA sequences in training
Issue -
State: open - Opened by dawnmy over 3 years ago
Labels: enhancement