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hzi-bifo
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RiboDetector
Accurate and rapid RiboRNA sequences Detector based on deep learning
GNU General Public License v3.0
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Log file/progress formatting for better readability
#52
mckellardw
opened
1 month ago
2
RiboDetector for barcoded libraries
#51
mckellardw
closed
2 months ago
2
Mouse data compatibility
#50
mmiots9
closed
3 months ago
2
No classification at all for some data and classification for some
#49
EorgeKit
closed
3 months ago
6
Read Length question
#48
singhbhavya
closed
3 months ago
1
fix the issue caused by less random default socket addresses for multiprocessing.Manager()
#47
dawnmy
closed
3 months ago
0
Address already in use
#46
lucacozzuto
closed
3 months ago
5
Classification of the rRNA removed seqeunces
#45
LeoVincenzi
closed
3 months ago
3
Tuple range error
#44
mwylerCH
closed
6 months ago
3
Can we apply this tool for custom reference sequences?
#43
ssun1116
closed
7 months ago
2
ValueError:you are required to explicitly set the providers parameter when instantiating InferenceSession
#42
Abelcanc3rhack3r
closed
7 months ago
1
Can we use Ribodetector for rRNA quantification in scRNASeq?
#41
Rohit-Satyam
closed
10 months ago
1
RuntimeError: indices should be either on cpu or on the same device as the indexed tensor (cpu)
#40
caldodge
closed
7 months ago
9
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
#39
li1311139481
closed
1 year ago
2
Retrive the filtered out sequences
#38
LeoVincenzi
closed
1 year ago
2
RiboDetector is identifying reads generated from ChrX and ChrY as rRNA reads
#37
rajanbit
closed
11 months ago
4
[ERROR] Unable to run ribodetector on a remote server: No visible CUDA devices!
#36
jwilliams648
closed
9 months ago
1
Change the log info, from detect_cpu to ribodetector_cpu
#35
dawnmy
closed
7 months ago
0
RiboDetector is not working on GPU mode
#34
Nirmal2310
closed
1 year ago
4
Ability to produce a log file that can be easily processed by MultiQC
#33
Rohit-Satyam
closed
6 months ago
18
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
#32
Rohit-Satyam
closed
1 year ago
2
ribodetector_cpu hangs with SLURM
#31
gianfilippo
closed
1 year ago
4
Recommendations on running RiboDetector twice on the fastq files?
#30
resol341
closed
1 year ago
2
ribodetector_cpu classifies and outputs more reads in the end than there were in the input data to begin with
#29
erzakiev
closed
1 year ago
13
Which organism?
#28
Homap
closed
1 year ago
1
Chunk size question
#27
caity-s
closed
1 year ago
3
gzip is very slow
#26
alienzj
closed
1 year ago
1
Question
#25
deoliveira86
closed
1 year ago
2
Using RiboDetector on assembled contigs?
#24
natashagriffin
closed
1 year ago
2
question regarding confidence of -e norrna option
#23
caity-s
closed
1 year ago
4
docker image for 0.2.6
#22
NicoleGruenheit
closed
1 year ago
3
False postivies when using on metagenomic data?
#21
rezenman
closed
1 year ago
6
About read length
#20
gouwei1
closed
1 year ago
2
Is it possible using Ribodector on metagenomic reads
#19
lideyongJNU
closed
2 years ago
1
CPU mode hangs with macOS
#18
omicz
closed
1 year ago
6
cpu vs. gpu performance
#17
ARW-UBT
closed
1 year ago
4
read length should be not smaller than 50, but ribo-seq reads are ~30 bp
#16
huguanjing
closed
1 year ago
4
Installation error in conda environemnt
#15
ARW-UBT
closed
2 years ago
6
Add model eval?
#14
dawnmy
closed
1 year ago
1
In CPU mode, smaller chunk_size does not reduce the memory use.
#13
dawnmy
closed
2 years ago
3
Memory Calculation Doubts
#12
magcurly
closed
2 years ago
7
no rRNA sequences were detected in an almost complete genome
#11
ThomasYJK555
closed
2 years ago
2
Add chunk size support for loading the sequences to reduce memory use for large files
#10
dawnmy
closed
2 years ago
2
Memory issues with RiboDetector
#9
akrinos
closed
2 years ago
23
GPU with higher CUDA version can not be used within old pytorch
#8
sixvable
closed
2 years ago
12
Lost reads?
#7
sjaenick
closed
2 years ago
2
Process hangs in CPU detection step
#6
sjaenick
closed
2 years ago
23
Optimize for CPU which supports AVX2 instruction
#5
dawnmy
opened
2 years ago
0
Training for next main release
#4
dawnmy
closed
2 years ago
0
Add tests
#3
dawnmy
opened
2 years ago
0
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