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261
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When should I normalize and subset adata objects in scanpy?
scanpy
scRNA-seq
single-cell
updated 22 days ago by
LChart
4.2k • written 22 days ago by
bioinfo
▴ 150
0
votes
1
reply
232
views
How to choose cells that co-express several genes with scanpy?
scanpy
scRNA-seq
single-cell
updated 5 weeks ago by
LChart
4.2k • written 5 weeks ago by
bioinfo
▴ 150
0
votes
0
replies
143
views
How to run trajectory analysis with only one cell type using palantir?
palantir
scanpy
7 weeks ago by
bioinfo
▴ 150
2
votes
1
reply
217
views
Do I need to remove doublets after before or after running hashsolo?
hashsolo
scanpy
scrublet
updated 7 weeks ago by
tothepoint
▴ 890 • written 7 weeks ago by
bioinfo
▴ 150
0
votes
0
replies
240
views
Comment:
Comment: How can I import an unindexed human gtf file in IGV?
8 weeks ago by
bioinfo
▴ 150
0
votes
2
replies
240
views
How can I import an unindexed human gtf file in IGV?
igv
8 weeks ago by
bioinfo
▴ 150
0
votes
0
replies
521
views
Comment:
Comment: Why am I getting such a big difference in alignment rates in kallisto?
11 weeks ago by
bioinfo
▴ 150
0
votes
1
reply
521
views
Comment:
Comment: Why am I getting such a big difference in alignment rates in kallisto?
11 weeks ago by
bioinfo
▴ 150
0
votes
1
reply
521
views
Comment:
Comment: Why am I getting such a big difference in alignment rates in kallisto?
11 weeks ago by
bioinfo
▴ 150
0
votes
6
replies
521
views
Why am I getting such a big difference in alignment rates in kallisto?
kallisto
ensembl
11 weeks ago by
bioinfo
▴ 150
0
votes
1
reply
348
views
Comment:
Comment: Where are the illumina adapters on Trimmomatic take from?
3 months ago by
bioinfo
▴ 150
1
vote
3
replies
348
views
Where are the illumina adapters on Trimmomatic take from?
rna-seq
trimmomatic
updated 3 months ago by
GenoMax
145k • written 3 months ago by
bioinfo
▴ 150
0
votes
0
replies
402
views
Comment:
Comment: Why does assigning genes with biomart give me different values than using a tran
3 months ago by
bioinfo
▴ 150
2
votes
2
replies
402
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
3 months ago by
bioinfo
▴ 150
0
votes
1
reply
839
views
Comment:
Comment: How should I make kallisto indexes?
4 months ago by
bioinfo
▴ 150
1
vote
5
replies
839
views
How should I make kallisto indexes?
kallisto
updated 4 months ago by
dsull
★ 6.8k • written 4 months ago by
bioinfo
▴ 150
0
votes
0
replies
406
views
Comment:
Comment: Can I compare kallisto counts from samples with different amount of reads?
4 months ago by
bioinfo
▴ 150
0
votes
0
replies
463
views
Comment:
Comment: How to row normalize a matrixplot?
4 months ago by
bioinfo
▴ 150
1
vote
2
replies
406
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
4 months ago by
bioinfo
▴ 150
2
votes
2
replies
463
views
How to row normalize a matrixplot?
scRNA-seq
RNA-seq
single-cell
scanpy
4 months ago by
bioinfo
▴ 150
0
votes
1
reply
515
views
How to do DE between cells expressing specific gene in scanpy?
scRNA-seq
single-cell
scanpy
updated 4 months ago by
Ram
44k • written 4 months ago by
bioinfo
▴ 150
0
votes
0
replies
475
views
Comment:
Comment: How to compare bulk RNA seq data demultiplexed in different ways?
5 months ago by
bioinfo
▴ 150
0
votes
1
reply
475
views
Comment:
Comment: How to compare bulk RNA seq data demultiplexed in different ways?
5 months ago by
bioinfo
▴ 150
0
votes
5
replies
475
views
How to compare bulk RNA seq data demultiplexed in different ways?
RNA-seq
updated 4 months ago by
Ram
44k • written 5 months ago by
bioinfo
▴ 150
0
votes
1
reply
791
views
Comment:
Comment: How does kallisto handle multi mapped reads?
6 months ago by
bioinfo
▴ 150
0
votes
1
reply
791
views
Comment:
Comment: How does kallisto handle multi mapped reads?
6 months ago by
bioinfo
▴ 150
3
votes
7
replies
791
views
How does kallisto handle multi mapped reads?
kallisto
updated 6 months ago by
dsull
★ 6.8k • written 6 months ago by
bioinfo
▴ 150
0
votes
2
replies
550
views
How to add motifs in cellranger-arc reference?
gtf
scRNAseq
fasta
cellranger
updated 4 months ago by
Ehsan
• 0 • written 6 months ago by
bioinfo
▴ 150
0
votes
0
replies
376
views
How to do KEGG pathway analysis when I have a gene with multiple entrez IDs?
biomart
kegg
deseq2
9 months ago by
bioinfo
▴ 150
4
votes
2
replies
823
views
Does DESeq2 correct for library size when importing the counts with DESeqDataSetFromMatrix?
rna-seq
deseq2
updated 9 months ago by
i.sudbery
20k • written 9 months ago by
bioinfo
▴ 150
0
votes
1
reply
1.2k
views
Comment:
Comment: How much adapters is it ok to keep in my samples after RNA seq?
9 months ago by
bioinfo
▴ 150
0
votes
1
reply
1.2k
views
Comment:
Comment: How much adapters is it ok to keep in my samples after RNA seq?
9 months ago by
bioinfo
▴ 150
0
votes
1
reply
1.2k
views
Comment:
Comment: How much adapters is it ok to keep in my samples after RNA seq?
9 months ago by
bioinfo
▴ 150
3
votes
7
replies
1.2k
views
How much adapters is it ok to keep in my samples after RNA seq?
RNA-seq
illumina
adapters
updated 4 months ago by
Ram
44k • written 9 months ago by
bioinfo
▴ 150
0
votes
0
replies
860
views
Comment:
Comment: Why am I getting different results with kallisto?
9 months ago by
bioinfo
▴ 150
0
votes
1
reply
860
views
Comment:
Comment: Why am I getting different results with kallisto?
9 months ago by
bioinfo
▴ 150
0
votes
1
reply
860
views
Comment:
Comment: Why am I getting different results with kallisto?
9 months ago by
bioinfo
▴ 150
3
votes
4
replies
860
views
Why am I getting different results with kallisto?
kallisto
9 months ago by
bioinfo
▴ 150
0
votes
1
reply
656
views
Comment:
Comment: Are truseq adapter sequences picked up by FASTQC?
9 months ago by
bioinfo
▴ 150
2
votes
3
replies
656
views
Are truseq adapter sequences picked up by FASTQC?
fastqc
truseq
updated 9 months ago by
GenoMax
145k • written 9 months ago by
bioinfo
▴ 150
0
votes
0
replies
424
views
How to convert dataframe properly to anndata?
single-cell
python
anndata
updated 4 months ago by
Ram
44k • written 10 months ago by
bioinfo
▴ 150
0
votes
0
replies
419
views
How to import filtered_tf_bc_matrix and add it to my anndata object?
python
anndata
atac-seq
updated 4 months ago by
Ram
44k • written 10 months ago by
bioinfo
▴ 150
0
votes
0
replies
385
views
How to subsample ATAC fragment file?
single-cell
atac-seq
scRNA-seq
updated 4 months ago by
Ram
44k • written 10 months ago by
bioinfo
▴ 150
0
votes
0
replies
872
views
Comment:
Comment: How to assign gene names after kallisto when I add GFP?
10 months ago by
bioinfo
▴ 150
0
votes
1
reply
872
views
Comment:
Comment: How to assign gene names after kallisto when I add GFP?
10 months ago by
bioinfo
▴ 150
0
votes
2
replies
2.0k
views
Removing constant/zero columns for PCA?
R
pca
updated 10 months ago by
Mensur Dlakic
★ 28k • written 10 months ago by
bioinfo
▴ 150
1
vote
4
replies
872
views
How to assign gene names after kallisto when I add GFP?
tximport
RNA-seq
kallisto
10 months ago by
bioinfo
▴ 150
0
votes
0
replies
2.8k
views
Comment:
Comment: How to plot proportion of cells in each cluster with scanpy?
11 months ago by
bioinfo
▴ 150
0
votes
0
replies
2.8k
views
Comment:
Comment: How to plot proportion of cells in each cluster with scanpy?
11 months ago by
bioinfo
▴ 150
1
vote
8
replies
2.8k
views
How to plot proportion of cells in each cluster with scanpy?
scRNA-seq
scanpy
single-cell
11 months ago by
bioinfo
▴ 150
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