Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Profile
Posts
Awards
Show
all
questions
tools
blogs
news
tutorials
forum
answers
comments
Showing :
questions
3
votes
2
replies
389
views
DESeq2 outliers-should I be concerned?
deseq2
updated 5 days ago by
ATpoint
88k • written 7 days ago by
bioinfo
▴ 150
0
votes
2
replies
349
views
Kallisto to tximport to deseq2
enseml
deseq2
Kallisto
updated 13 days ago by
GenoMax
151k • written 13 days ago by
bioinfo
▴ 150
0
votes
2
replies
338
views
Question about assigning gene names, tximport and DESeq2
tximport
deseq2
6 weeks ago by
bioinfo
▴ 150
1
vote
3
replies
1.7k
views
How to use harmony with scanpy?
scanpy
harmony
updated 12 weeks ago by
Rezin
• 0 • written 3 months ago by
bioinfo
▴ 150
2
votes
2
replies
560
views
Should I not have any adapters after trimming?
RNA-seq
updated 3 months ago by
swbarnes2
14k • written 3 months ago by
bioinfo
▴ 150
0
votes
0
replies
312
views
Does the order of HTOs matter?
hashsolo
scanpy
4 months ago by
bioinfo
▴ 150
0
votes
0
replies
278
views
Regression and scaling in scanpy
scanpy
5 months ago by
bioinfo
▴ 150
0
votes
1
reply
812
views
When should I normalize and subset adata objects in scanpy?
scanpy
scRNA-seq
single-cell
updated 9 months ago by
LChart
4.9k • written 9 months ago by
bioinfo
▴ 150
2
votes
1
reply
541
views
How to choose cells that co-express several genes with scanpy?
scanpy
scRNA-seq
single-cell
updated 10 months ago by
LChart
4.9k • written 10 months ago by
bioinfo
▴ 150
0
votes
0
replies
312
views
How to run trajectory analysis with only one cell type using palantir?
palantir
scanpy
10 months ago by
bioinfo
▴ 150
2
votes
1
reply
566
views
Do I need to remove doublets after before or after running hashsolo?
hashsolo
scanpy
scrublet
updated 10 months ago by
tothepoint
▴ 940 • written 10 months ago by
bioinfo
▴ 150
0
votes
2
replies
570
views
How can I import an unindexed human gtf file in IGV?
igv
10 months ago by
bioinfo
▴ 150
0
votes
6
replies
1.0k
views
Why am I getting such a big difference in alignment rates in kallisto?
kallisto
ensembl
11 months ago by
bioinfo
▴ 150
1
vote
3
replies
750
views
Where are the illumina adapters on Trimmomatic take from?
rna-seq
trimmomatic
updated 12 months ago by
GenoMax
151k • written 12 months ago by
bioinfo
▴ 150
2
votes
3
replies
816
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
7 months ago by
bioinfo
▴ 150
1
vote
5
replies
1.8k
views
How should I make kallisto indexes?
kallisto
updated 13 months ago by
dsull
★ 7.6k • written 13 months ago by
bioinfo
▴ 150
1
vote
2
replies
682
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
13 months ago by
bioinfo
▴ 150
2
votes
2
replies
854
views
How to row normalize a matrixplot?
scRNA-seq
RNA-seq
single-cell
scanpy
13 months ago by
bioinfo
▴ 150
0
votes
1
reply
1.1k
views
How to do DE between cells expressing specific gene in scanpy?
scRNA-seq
single-cell
scanpy
updated 13 months ago by
Ram
45k • written 13 months ago by
bioinfo
▴ 150
0
votes
5
replies
947
views
How to compare bulk RNA seq data demultiplexed in different ways?
RNA-seq
updated 13 months ago by
Ram
45k • written 13 months ago by
bioinfo
▴ 150
3
votes
7
replies
1.4k
views
How does kallisto handle multi mapped reads?
kallisto
updated 15 months ago by
dsull
★ 7.6k • written 15 months ago by
bioinfo
▴ 150
0
votes
2
replies
937
views
How to add motifs in cellranger-arc reference?
gtf
scRNAseq
fasta
cellranger
updated 13 months ago by
Ehsan
• 0 • written 15 months ago by
bioinfo
▴ 150
0
votes
0
replies
568
views
How to do KEGG pathway analysis when I have a gene with multiple entrez IDs?
biomart
kegg
deseq2
18 months ago by
bioinfo
▴ 150
4
votes
2
replies
1.1k
views
Does DESeq2 correct for library size when importing the counts with DESeqDataSetFromMatrix?
rna-seq
deseq2
updated 18 months ago by
i.sudbery
21k • written 18 months ago by
bioinfo
▴ 150
3
votes
7
replies
1.8k
views
How much adapters is it ok to keep in my samples after RNA seq?
RNA-seq
illumina
adapters
updated 13 months ago by
Ram
45k • written 18 months ago by
bioinfo
▴ 150
3
votes
4
replies
1.3k
views
Why am I getting different results with kallisto?
kallisto
18 months ago by
bioinfo
▴ 150
2
votes
3
replies
985
views
Are truseq adapter sequences picked up by FASTQC?
fastqc
truseq
updated 18 months ago by
GenoMax
151k • written 18 months ago by
bioinfo
▴ 150
0
votes
0
replies
636
views
How to convert dataframe properly to anndata?
single-cell
python
anndata
updated 13 months ago by
Ram
45k • written 19 months ago by
bioinfo
▴ 150
0
votes
0
replies
584
views
How to import filtered_tf_bc_matrix and add it to my anndata object?
python
anndata
atac-seq
updated 13 months ago by
Ram
45k • written 19 months ago by
bioinfo
▴ 150
0
votes
0
replies
531
views
How to subsample ATAC fragment file?
single-cell
atac-seq
scRNA-seq
updated 13 months ago by
Ram
45k • written 19 months ago by
bioinfo
▴ 150
0
votes
2
replies
3.3k
views
Removing constant/zero columns for PCA?
R
pca
updated 19 months ago by
Mensur Dlakic
★ 29k • written 19 months ago by
bioinfo
▴ 150
1
vote
4
replies
1.4k
views
How to assign gene names after kallisto when I add GFP?
tximport
RNA-seq
kallisto
19 months ago by
bioinfo
▴ 150
1
vote
8
replies
4.9k
views
How to plot proportion of cells in each cluster with scanpy?
scRNA-seq
scanpy
single-cell
20 months ago by
bioinfo
▴ 150
5
votes
2
replies
1.1k
views
How to calculate GC content of reads that mapped to a specific gene?
STAR
RNA-seq
20 months ago by
bioinfo
▴ 150
0
votes
8
replies
1.5k
views
Can the DESeq2 object for paired data be set with design= ~ batch + condition?
rna-seq
deseq2
21 months ago by
bioinfo
▴ 150
1
vote
1
reply
1.1k
views
Do I need to perform basic filtering before using scrublet?
scanpy
scrublet
updated 21 months ago by
GenoMax
151k • written 21 months ago by
bioinfo
▴ 150
0
votes
2
replies
2.1k
views
How to choose threshold for scrublet?
rna-seq
scrublet
21 months ago by
bioinfo
▴ 150
1
vote
5
replies
1.9k
views
Questions about per base sequence quality and GC content.
fastqc
fastq
seq
RNA
21 months ago by
bioinfo
▴ 150
3
votes
3
replies
1.2k
views
How to assign gene names to ensembl IDs if species not in Biomart
biomart
ensembl
21 months ago by
bioinfo
▴ 150
0
votes
4
replies
4.1k
views
Why do I need to sort and index gtf file for IGV?
igv
updated 22 months ago by
ATpoint
88k • written 22 months ago by
bioinfo
▴ 150
3
votes
3
replies
1.1k
views
Where can I find the --chromosomes file for kallisto?
kallisto
updated 22 months ago by
GenoMax
151k • written 22 months ago by
bioinfo
▴ 150
3
votes
2
replies
1.0k
views
How to figure out adapter sequences in RNA seq?
adapters
rna-seq
updated 23 months ago by
rfran010
★ 1.5k • written 23 months ago by
bioinfo
▴ 150
1
vote
0
replies
569
views
How does kallisto genomebam handle multi mapping reads?
kallisto
updated 23 months ago by
Ram
45k • written 23 months ago by
bioinfo
▴ 150
4
votes
5
replies
1.3k
views
Does adding reads cause batch effects?
kallisto
RNAseq
23 months ago by
bioinfo
▴ 150
0
votes
0
replies
745
views
Do I need to do QC before demultiplexing hashtags with hashsolo?
scanpy
hashtag
hashsolo
RNAseq
2.1 years ago by
bioinfo
▴ 150
1
vote
3
replies
2.1k
views
How to demultiplex data with totalseq B antibodies using hashsolo?
cellranger.
seq
hashsolo
rna
2.1 years ago by
bioinfo
▴ 150
0
votes
2
replies
929
views
Do I need to specify the introns on the gtf file for cellranger?
fasta
gtf
cellranger
scRNAseq
updated 2.1 years ago by
GenoMax
151k • written 2.1 years ago by
bioinfo
▴ 150
3
votes
1
reply
885
views
Can I normalize several samples with DESeq2 and then do pairwise comparisons?
deseq2
rna-seq
updated 2.1 years ago by
rpolicastro
13k • written 2.1 years ago by
bioinfo
▴ 150
1
vote
1
reply
815
views
Do indexes made with cDNA fasta file contain only mRNAs?
ensembl
kallisto
updated 2.2 years ago by
dsull
★ 7.6k • written 2.2 years ago by
bioinfo
▴ 150
0
votes
0
replies
525
views
How to analyze SCRNA seq data labelled with LARRY?
single
lineage
RNA
tracing
LARRY
updated 2.2 years ago by
GenoMax
151k • written 2.2 years ago by
bioinfo
▴ 150
83 results • Page
1 of 2
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6