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Showing :
questions
0
votes
0
replies
475
views
Concatenation of adata and losing .var
single
seq
cell
RNA
scanpy
3 months ago by
bioinfo
▴ 160
0
votes
1
reply
807
views
How to run trajectory analysis with only one cell type using palantir?
palantir
scanpy
updated 4 months ago by
npont
▴ 20 • written 16 months ago by
bioinfo
▴ 160
1
vote
4
replies
719
views
How to add GFP in STAR reference?
STAR
updated 5 months ago by
GenoMax
154k • written 5 months ago by
bioinfo
▴ 160
0
votes
3
replies
1.1k
views
Random seed in scanpy
scanpy
scRNAseq
single-cell
updated 5 months ago by
ATpoint
90k • written 5 months ago by
bioinfo
▴ 160
4
votes
2
replies
824
views
DESeq2 outliers-should I be concerned?
deseq2
updated 5 months ago by
ATpoint
90k • written 5 months ago by
bioinfo
▴ 160
0
votes
2
replies
747
views
Kallisto to tximport to deseq2
enseml
deseq2
Kallisto
updated 6 months ago by
GenoMax
154k • written 6 months ago by
bioinfo
▴ 160
0
votes
2
replies
708
views
Question about assigning gene names, tximport and DESeq2
tximport
deseq2
7 months ago by
bioinfo
▴ 160
1
vote
3
replies
4.4k
views
How to use harmony with scanpy?
scanpy
harmony
updated 8 months ago by
Rezin
• 0 • written 8 months ago by
bioinfo
▴ 160
2
votes
2
replies
915
views
Should I not have any adapters after trimming?
RNA-seq
updated 8 months ago by
swbarnes2
15k • written 8 months ago by
bioinfo
▴ 160
0
votes
0
replies
503
views
Does the order of HTOs matter?
hashsolo
scanpy
10 months ago by
bioinfo
▴ 160
0
votes
0
replies
622
views
Regression and scaling in scanpy
scanpy
11 months ago by
bioinfo
▴ 160
0
votes
1
reply
1.3k
views
When should I normalize and subset adata objects in scanpy?
scanpy
scRNA-seq
single-cell
updated 15 months ago by
LChart
5.2k • written 15 months ago by
bioinfo
▴ 160
2
votes
1
reply
828
views
How to choose cells that co-express several genes with scanpy?
scanpy
scRNA-seq
single-cell
updated 15 months ago by
LChart
5.2k • written 15 months ago by
bioinfo
▴ 160
2
votes
1
reply
853
views
Do I need to remove doublets after before or after running hashsolo?
hashsolo
scanpy
scrublet
updated 16 months ago by
tothepoint
▴ 940 • written 16 months ago by
bioinfo
▴ 160
0
votes
2
replies
834
views
How can I import an unindexed human gtf file in IGV?
igv
16 months ago by
bioinfo
▴ 160
0
votes
6
replies
1.5k
views
Why am I getting such a big difference in alignment rates in kallisto?
kallisto
ensembl
17 months ago by
bioinfo
▴ 160
1
vote
3
replies
1.1k
views
Where are the illumina adapters on Trimmomatic take from?
rna-seq
trimmomatic
updated 17 months ago by
GenoMax
154k • written 17 months ago by
bioinfo
▴ 160
2
votes
3
replies
1.1k
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
13 months ago by
bioinfo
▴ 160
1
vote
5
replies
2.6k
views
How should I make kallisto indexes?
kallisto
updated 18 months ago by
dsull
★ 7.8k • written 19 months ago by
bioinfo
▴ 160
1
vote
2
replies
983
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
18 months ago by
bioinfo
▴ 160
2
votes
2
replies
1.2k
views
How to row normalize a matrixplot?
scRNA-seq
RNA-seq
single-cell
scanpy
19 months ago by
bioinfo
▴ 160
0
votes
1
reply
1.6k
views
How to do DE between cells expressing specific gene in scanpy?
scRNA-seq
single-cell
scanpy
updated 19 months ago by
Ram
45k • written 19 months ago by
bioinfo
▴ 160
0
votes
5
replies
1.3k
views
How to compare bulk RNA seq data demultiplexed in different ways?
RNA-seq
updated 19 months ago by
Ram
45k • written 19 months ago by
bioinfo
▴ 160
3
votes
7
replies
2.0k
views
How does kallisto handle multi mapped reads?
kallisto
updated 20 months ago by
dsull
★ 7.8k • written 20 months ago by
bioinfo
▴ 160
0
votes
2
replies
1.4k
views
How to add motifs in cellranger-arc reference?
gtf
scRNAseq
fasta
cellranger
updated 18 months ago by
Ehsan
• 0 • written 20 months ago by
bioinfo
▴ 160
0
votes
0
replies
800
views
How to do KEGG pathway analysis when I have a gene with multiple entrez IDs?
biomart
kegg
deseq2
23 months ago by
bioinfo
▴ 160
4
votes
2
replies
1.5k
views
Does DESeq2 correct for library size when importing the counts with DESeqDataSetFromMatrix?
rna-seq
deseq2
updated 24 months ago by
i.sudbery
22k • written 24 months ago by
bioinfo
▴ 160
3
votes
7
replies
2.3k
views
How much adapters is it ok to keep in my samples after RNA seq?
RNA-seq
illumina
adapters
updated 19 months ago by
Ram
45k • written 24 months ago by
bioinfo
▴ 160
3
votes
4
replies
1.7k
views
Why am I getting different results with kallisto?
kallisto
24 months ago by
bioinfo
▴ 160
2
votes
3
replies
1.4k
views
Are truseq adapter sequences picked up by FASTQC?
fastqc
truseq
updated 2.0 years ago by
GenoMax
154k • written 2.0 years ago by
bioinfo
▴ 160
0
votes
0
replies
845
views
How to convert dataframe properly to anndata?
single-cell
python
anndata
updated 19 months ago by
Ram
45k • written 2.0 years ago by
bioinfo
▴ 160
0
votes
0
replies
816
views
How to import filtered_tf_bc_matrix and add it to my anndata object?
python
anndata
atac-seq
updated 19 months ago by
Ram
45k • written 2.0 years ago by
bioinfo
▴ 160
0
votes
0
replies
683
views
How to subsample ATAC fragment file?
single-cell
atac-seq
scRNA-seq
updated 19 months ago by
Ram
45k • written 2.0 years ago by
bioinfo
▴ 160
0
votes
2
replies
4.1k
views
Removing constant/zero columns for PCA?
R
pca
updated 2.1 years ago by
Mensur Dlakic
★ 30k • written 2.1 years ago by
bioinfo
▴ 160
1
vote
4
replies
1.9k
views
How to assign gene names after kallisto when I add GFP?
tximport
RNA-seq
kallisto
2.1 years ago by
bioinfo
▴ 160
1
vote
8
replies
6.3k
views
How to plot proportion of cells in each cluster with scanpy?
scRNA-seq
scanpy
single-cell
2.1 years ago by
bioinfo
▴ 160
5
votes
2
replies
1.5k
views
How to calculate GC content of reads that mapped to a specific gene?
STAR
RNA-seq
2.2 years ago by
bioinfo
▴ 160
0
votes
8
replies
2.0k
views
Can the DESeq2 object for paired data be set with design= ~ batch + condition?
rna-seq
deseq2
2.2 years ago by
bioinfo
▴ 160
1
vote
1
reply
1.5k
views
Do I need to perform basic filtering before using scrublet?
scanpy
scrublet
updated 2.2 years ago by
GenoMax
154k • written 2.2 years ago by
bioinfo
▴ 160
0
votes
2
replies
3.0k
views
How to choose threshold for scrublet?
rna-seq
scrublet
2.2 years ago by
bioinfo
▴ 160
1
vote
5
replies
2.6k
views
Questions about per base sequence quality and GC content.
fastqc
fastq
seq
RNA
2.2 years ago by
bioinfo
▴ 160
3
votes
3
replies
1.5k
views
How to assign gene names to ensembl IDs if species not in Biomart
biomart
ensembl
2.2 years ago by
bioinfo
▴ 160
0
votes
4
replies
5.3k
views
Why do I need to sort and index gtf file for IGV?
igv
updated 2.3 years ago by
ATpoint
90k • written 2.3 years ago by
bioinfo
▴ 160
3
votes
3
replies
1.4k
views
Where can I find the --chromosomes file for kallisto?
kallisto
updated 2.3 years ago by
GenoMax
154k • written 2.3 years ago by
bioinfo
▴ 160
3
votes
2
replies
1.4k
views
How to figure out adapter sequences in RNA seq?
adapters
rna-seq
updated 2.4 years ago by
rfran010
★ 1.7k • written 2.4 years ago by
bioinfo
▴ 160
1
vote
0
replies
730
views
How does kallisto genomebam handle multi mapping reads?
kallisto
updated 2.4 years ago by
Ram
45k • written 2.4 years ago by
bioinfo
▴ 160
4
votes
5
replies
1.6k
views
Does adding reads cause batch effects?
kallisto
RNAseq
2.4 years ago by
bioinfo
▴ 160
0
votes
0
replies
921
views
Do I need to do QC before demultiplexing hashtags with hashsolo?
scanpy
hashtag
hashsolo
RNAseq
2.5 years ago by
bioinfo
▴ 160
1
vote
3
replies
2.6k
views
How to demultiplex data with totalseq B antibodies using hashsolo?
cellranger.
seq
hashsolo
rna
2.5 years ago by
bioinfo
▴ 160
0
votes
2
replies
1.2k
views
Do I need to specify the introns on the gtf file for cellranger?
fasta
gtf
cellranger
scRNAseq
updated 2.6 years ago by
GenoMax
154k • written 2.6 years ago by
bioinfo
▴ 160
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