另外,Seurat最近新出的版本version 4.0改变了function RunUMAP()的默认方法选择。在RunUMAP中提供了两种运行方法,一是通过uwot R package, 另一种是Seurat包装的python umap-learn package。在之前的版本中,默认的方法是umap-learn, 而在最新的4.0版本中改成了uwot。因此如果想继续用umap-learn的话,需要将umap.metho...
mainChromosomes <- paste0("chr", c(1:19, "X", "Y", "M")) mainChrSeq <- lapply(mainChromosomes, function(x) BSgenome.Mmusculus.UCSC.mm10[[x]]) names(mainChrSeq) <- mainChromosomes mainChrSeqSet <- DNAStringSet(mainChrSeq) mainChrSeqSet mainChrSeqSet 现在我们有了一个 DNAStringS...
source_int = [[source_letter_to_int.get(letter, source_letter_to_int['<UNK>'])for letter in line] for line in source_data.split('\n')]target_int = [[target_letter_to_int.get(letter, target_letter_to_int['<UNK>'])for letter in line] + [target_letter_to_int['<EOS>']] fo...
Overlap of peaks and annotated genes genes= lapply(peakAnnoList, function(i) as.data.frame(i)$geneId) vennplot(genes) 
from __future__ import print_function 4 from __future__ importunicode_literals 5 6 import torch 7 import torch.nn as nn 8 import torch.nn.functional as F 9 import re 10 import os 11 import unicodedata 12 import numpy as np ...
("SqlSatelliteCall", params)\r\n File "C:\Program Files\Microsoft SQL Server\MSSQL15.SQL01\PYTHON_SERVICES\lib\site-packages\revoscalepy\RxSerializable.py", line 375, in rx_native_call\r\n ret = px_call(functionname, params)\r\nRuntimeError: revoscalepy function failed.\r (39005)'...
CITE-seq-Count是用Python搭建的工具,所以可以用pip安装: pip install CITE-seq-Count==1.4.3 How to use it CITE-seq-Count -R1 TAGS_R1.fastq.gz -R2 TAGS_R2.fastq.gz -t TAG_LIST.csv -cbf X1 -cbl X2 -umif Y1 -umil Y2 -cells EXPECTED_CELLS -o OUTFOLDER ...
forlogit,target,weightinzip(logits,targets,weights): ifsoftmax_loss_functionisNone: # TODO(irving,ebrevdo): This reshape is needed because # sequence_loss_by_example is called with scalars sometimes, which # violates our general scalar strictness policy. ...
_ import divisionfrom __future__ import print_functionimport copy# We disable pylint because we need python3 compatibility.from six.moves import xrange # pylint: disable=redefined-builtinfrom six.moves import zip # pylint: disable=redefined-builtin#core_rnn_cell在tensorflow/contrib/rnn/python/ops...
Afterwards, we checked for presence of the UMI sequence (with or without addition of GGG overhang) in the genomic window using R’s fuzzy string matching function (allowing 0, 1 or 2 mismatches). This identification procedure of artifactual UMI reads was also implemented in Python3 to process...