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217 Open 153 Closed
217 Open 153 Closed
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Issues list

Integrating Ambient RNA Removal (CellBender) into Velocity Analysis
#403 opened Aug 21, 2024 by Evenlyeven
Merging multiple loom files with different reference genome
#402 opened Aug 16, 2024 by yechanYS
Retriving genes with caracterisitic velocity behavior accorindg to latent time
#401 opened Aug 2, 2024 by Dalhte
When calculate the unspliced reads, does UTR region included or not?
#400 opened Jul 29, 2024 by DieTANG
Package dependency problem on NumPy
#397 opened Jul 1, 2024 by jasonleongbio
2
How to get fastq header information of spliced and unspliced 10X short reads
#396 opened Jun 25, 2024 by wenhu0701
Incorrect trimming of chromosome name leads to IOError(f"Input .bam file should be chromosome-sorted. (Hint: use samtools sort {bamfile})")
#395 opened Jun 25, 2024 by kepbod
3
Mark spliced/unspliced reads on original BAM file
#394 opened Jun 5, 2024 by taffy-miao
Seems like a typo.
#393 opened May 29, 2024 by chenqiuhao
Additional gene problem
#392 opened May 15, 2024 by Cadaqoes
Using spatial transcriptomics data on Velocyto.py generates lower counts than Space Ranger
#391 opened May 8, 2024 by biyang-bioinfo
Inquiry on the input for running "velocyto run10x"
#390 opened May 3, 2024 by daisyko
velocyto on filtered or raw matrix or from matrix corrected ?
#389 opened Apr 8, 2024 by Sirin24
WARNING - The .bam file refers to a chromosome not present in the annotation (.gtf) file
#388 opened Feb 28, 2024 by sekekeretsu
4
OSError: truncated file is occured in cellranger-5.0.1-dirty output.
#387 opened Feb 26, 2024 by ilovegreentea
index file
#386 opened Jan 13, 2024 by sherinesaber
1
how do i generate the repeat sequences masked gtf file from Ensembl?
#385 opened Jan 12, 2024 by erzakiev
When and when not to use "repeat annotation mask" in 10X?
#384 opened Dec 27, 2023 by denvercal1234GitHub
Question about latent parameter t
#383 opened Dec 20, 2023 by taffy-miao
BlockingIOError: [Errno 35] 'Resource temporarily unavailable' on Mac OS X
#382 opened Dec 13, 2023 by YitengDang
Unable to run velocyto: samtools issue
#380 opened Nov 11, 2023 by millerkaplanlab
1
TypeError: create() got an unexpected keyword argument 'matrix'
#379 opened Nov 11, 2023 by zcaiwei
Passing velocyto samtools memory for sorting step
#378 opened Nov 9, 2023 by wudustan
ImportError: speedboosted.cpython-38-x86_64-linux-gnu.so: undefined symbol: __log10_finite
#377 opened Nov 1, 2023 by lili03080317
2
Get tons of warnings when running
#376 opened Oct 23, 2023 by dingyaozhang
1
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