velocyto-team velocyto.py issues

velocyto-team / velocyto.py

RNA velocity estimation in Python

http://velocyto.org/velocyto.py/

BSD 2-Clause "Simplified" License

159 stars 83 forks source link

issues

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installation issue

#405 HSvitina opened 1 week ago
0
Unable to retrieve spliced/unspliced RNA from single nuclei isolation

#404 hyjforesight closed 1 week ago
1
Integrating Ambient RNA Removal (CellBender) into Velocity Analysis

#403 Evenlyeven opened 1 month ago
0
Merging multiple loom files with different reference genome

#402 yechanYS opened 1 month ago
0
Retriving genes with caracterisitic velocity behavior accorindg to latent time

#401 Dalhte opened 2 months ago
0
When calculate the unspliced reads, does UTR region included or not?

#400 DieTANG opened 2 months ago
0
Memory & run time issue run10x

#399 DelongZHOU closed 2 months ago
1
Velocyto ran successfully but main matrix is missing

#398 econnolly7 closed 2 months ago
2
Package dependency problem on NumPy

#397 jasonleongbio opened 3 months ago
2
How to get fastq header information of spliced and unspliced 10X short reads

#396 wenhu0701 opened 3 months ago
0
Incorrect trimming of chromosome name leads to IOError(f"Input .bam file should be chromosome-sorted. (Hint: use `samtools sort {bamfile}`)")

#395 kepbod opened 3 months ago
3
Mark spliced/unspliced reads on original BAM file

#394 taffy-miao opened 3 months ago
0
Seems like a typo.

#393 chenqiuhao opened 4 months ago
0
Additional gene problem

#392 Cadaqoes opened 4 months ago
0
Using spatial transcriptomics data on Velocyto.py generates lower counts than Space Ranger

#391 biyang-bioinfo opened 4 months ago
0
Inquiry on the input for running "velocyto run10x"

#390 daisyko opened 5 months ago
0
velocyto on filtered or raw matrix or from matrix corrected ?

#389 Sirin24 opened 5 months ago
0
WARNING - The .bam file refers to a chromosome not present in the annotation (.gtf) file

#388 sekekeretsu opened 7 months ago
4
OSError: truncated file is occured in cellranger-5.0.1-dirty output.

#387 ilovegreentea opened 7 months ago
0
index file

#386 sherinesaber opened 8 months ago
1
how do i generate the repeat sequences masked gtf file from Ensembl?

#385 erzakiev opened 8 months ago
0
When and when not to use "repeat annotation mask" in 10X?

#384 denvercal1234GitHub opened 9 months ago
0
Question about latent parameter t

#383 taffy-miao opened 9 months ago
0
BlockingIOError: [Errno 35] 'Resource temporarily unavailable' on Mac OS X

#382 YitengDang opened 9 months ago
0
[E::bgzf_read_block] Failed to read BGZF header at offset X

#381 YitengDang closed 9 months ago
1
Unable to run velocyto: samtools issue

#380 millerkaplanlab opened 10 months ago
1
TypeError: create() got an unexpected keyword argument 'matrix'

#379 zcaiwei opened 10 months ago
0
Passing velocyto samtools memory for sorting step

#378 wudustan opened 10 months ago
0
ImportError: speedboosted.cpython-38-x86_64-linux-gnu.so: undefined symbol: __log10_finite

#377 lili03080317 opened 11 months ago
3
Get tons of warnings when running

#376 dingyaozhang opened 11 months ago
1
Batch effects in combining multiple loom files

#375 anshu957 opened 12 months ago
2
ValueError: Column attribute 'Clusters' is not the same length (0) as number of columns in main matrix (3708)

#374 denvercal1234GitHub opened 1 year ago
0
Error in run10X: logging.debug(f"Example of barcode: {valid_bcs_list[0].split('-')[0]} and cell_id: {valid_cellid_list[0]}") - IndexError: list index out of range

#373 denvercal1234GitHub opened 1 year ago
1
AttributeError: 'NoneType' object has no attribute 'group'

#372 danli349 opened 1 year ago
0
Running velocyto on 10x Cell Ranger cloud-generated files

#371 schroeme closed 1 year ago
4
Testing

#370 milescsmith closed 1 year ago
0
Compatibility with non-string form for barcodes and UMIs

#369 weir12 opened 1 year ago
0
Multi-omic

#368 zhangqc723 opened 1 year ago
0
velocyto Index Out of Range

#367 TamaraSall opened 1 year ago
2
Issues running velocyto

#366 Battamama opened 1 year ago
1
Unexpected MemoryError: bam file #0 could not be sorted by cells.

#365 monica-nicolau opened 1 year ago
0
High % of unspliced from 10X scRNAseq in tissues

#364 denvercal1234GitHub opened 1 year ago
5
Do not resolve paths for bamfile and barcodes:

#363 tucano opened 1 year ago
0
how velocyto fits to cellrange-arc output

#362 zqmiao-mzq opened 1 year ago
2
meanings of layers

#361 songmingl opened 1 year ago
2
possorted_genome_bam.bam file not found in cellranger output folder

#360 tangybat opened 1 year ago
1
Error when running velocyto run-smartseq2

#359 ETAOIK opened 1 year ago
1
ERRORS when running velocyto: ERROR - This is an older version of cellranger, cannot check if the output are ready, make sure of this yourself! ERROR - Can not locate the barcodes.tsv file!

#358 AsyaTiho opened 1 year ago
2
gene name issue

#357 YichaoOU closed 1 year ago
1
CellRanger --include-introns

#356 GEmilioHO opened 1 year ago
0