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0
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When should I normalize and subset adata objects in scanpy?
scanpy scRNA-seq single-cell
updated 8 weeks ago by 4.3k • written 8 weeks ago by ▴ 150
0
votes
1
reply
256
views
How to choose cells that co-express several genes with scanpy?
scanpy scRNA-seq single-cell
updated 11 weeks ago by 4.3k • written 11 weeks ago by ▴ 150
0
votes
0
replies
159
views
How to run trajectory analysis with only one cell type using palantir?
palantir scanpy
3 months ago by bioinfo ▴ 150
2
votes
1
reply
245
views
Do I need to remove doublets after before or after running hashsolo?
hashsolo scanpy scrublet
updated 3 months ago by ▴ 930 • written 3 months ago by ▴ 150
0
votes
2
replies
263
views
How can I import an unindexed human gtf file in IGV?
igv
3 months ago by bioinfo ▴ 150
0
votes
6
replies
574
views
Why am I getting such a big difference in alignment rates in kallisto?
kallisto ensembl
3 months ago by bioinfo ▴ 150
1
vote
3
replies
387
views
Where are the illumina adapters on Trimmomatic take from?
rna-seq trimmomatic
updated 4 months ago by 146k • written 4 months ago by ▴ 150
2
votes
3
replies
514
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart RNAseq kallisto
9 days ago by bioinfo ▴ 150
1
vote
5
replies
961
views
How should I make kallisto indexes?
kallisto
updated 5 months ago by ★ 6.9k • written 5 months ago by ▴ 150
1
vote
2
replies
432
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq kallisto
5 months ago by bioinfo ▴ 150
2
votes
2
replies
512
views
How to row normalize a matrixplot?
scRNA-seq RNA-seq single-cell scanpy
5 months ago by bioinfo ▴ 150
0
votes
1
reply
599
views
How to do DE between cells expressing specific gene in scanpy?
scRNA-seq single-cell scanpy
updated 6 months ago by 44k • written 6 months ago by ▴ 150
0
votes
5
replies
519
views
How to compare bulk RNA seq data demultiplexed in different ways?
RNA-seq
updated 6 months ago by 44k • written 6 months ago by ▴ 150
3
votes
7
replies
866
views
How does kallisto handle multi mapped reads?
kallisto
updated 7 months ago by ★ 6.9k • written 7 months ago by ▴ 150
0
votes
2
replies
589
views
How to add motifs in cellranger-arc reference?
gtf scRNAseq fasta cellranger
updated 5 months ago by • 0 • written 7 months ago by ▴ 150
0
votes
0
replies
403
views
How to do KEGG pathway analysis when I have a gene with multiple entrez IDs?
biomart kegg deseq2
10 months ago by bioinfo ▴ 150
4
votes
2
replies
863
views
Does DESeq2 correct for library size when importing the counts with DESeqDataSetFromMatrix?
rna-seq deseq2
updated 10 months ago by 20k • written 10 months ago by ▴ 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 6 months ago by 44k • written 11 months ago by ▴ 150
3
votes
4
replies
906
views
Why am I getting different results with kallisto?
kallisto
11 months ago by bioinfo ▴ 150
2
votes
3
replies
697
views
Are truseq adapter sequences picked up by FASTQC?
fastqc truseq
updated 11 months ago by 146k • written 11 months ago by ▴ 150
0
votes
0
replies
445
views
How to convert dataframe properly to anndata?
single-cell python anndata
updated 6 months ago by 44k • written 11 months ago by ▴ 150
0
votes
0
replies
440
views
How to import filtered_tf_bc_matrix and add it to my anndata object?
python anndata atac-seq
updated 6 months ago by 44k • written 11 months ago by ▴ 150
0
votes
0
replies
406
views
How to subsample ATAC fragment file?
single-cell atac-seq scRNA-seq
updated 6 months ago by 44k • written 11 months ago by ▴ 150
0
votes
2
replies
2.2k
views
Removing constant/zero columns for PCA?
R pca
updated 12 months ago by ★ 28k • written 12 months ago by ▴ 150
1
vote
4
replies
927
views
How to assign gene names after kallisto when I add GFP?
tximport RNA-seq kallisto
11 months ago by bioinfo ▴ 150
1
vote
8
replies
3.1k
views
How to plot proportion of cells in each cluster with scanpy?
scRNA-seq scanpy single-cell
12 months ago by bioinfo ▴ 150
5
votes
2
replies
811
views
How to calculate GC content of reads that mapped to a specific gene?
STAR RNA-seq
13 months ago by bioinfo ▴ 150
0
votes
8
replies
1.1k
views
Can the DESeq2 object for paired data be set with design= ~ batch + condition?
rna-seq deseq2
13 months ago by bioinfo ▴ 150
1
vote
1
reply
777
views
Do I need to perform basic filtering before using scrublet?
scanpy scrublet
updated 13 months ago by 146k • written 13 months ago by ▴ 150
0
votes
2
replies
1.5k
views
How to choose threshold for scrublet?
rna-seq scrublet
13 months ago by bioinfo ▴ 150
1
vote
5
replies
1.2k
views
Questions about per base sequence quality and GC content.
fastqc fastq seq RNA
13 months ago by bioinfo ▴ 150
3
votes
3
replies
883
views
How to assign gene names to ensembl IDs if species not in Biomart
biomart ensembl
14 months ago by bioinfo ▴ 150
0
votes
4
replies
2.4k
views
Why do I need to sort and index gtf file for IGV?
igv
updated 14 months ago by 85k • written 14 months ago by ▴ 150
3
votes
3
replies
856
views
Where can I find the --chromosomes file for kallisto?
kallisto
updated 15 months ago by 146k • written 15 months ago by ▴ 150
3
votes
2
replies
734
views
How to figure out adapter sequences in RNA seq?
adapters rna-seq
updated 15 months ago by ★ 1.3k • written 15 months ago by ▴ 150
1
vote
0
replies
472
views
How does kallisto genomebam handle multi mapping reads?
kallisto
updated 16 months ago by 44k • written 16 months ago by ▴ 150
4
votes
5
replies
965
views
Does adding reads cause batch effects?
kallisto RNAseq
16 months ago by bioinfo ▴ 150
0
votes
0
replies
605
views
Do I need to do QC before demultiplexing hashtags with hashsolo?
scanpy hashtag hashsolo RNAseq
17 months ago by bioinfo ▴ 150
1
vote
3
replies
1.6k
views
How to demultiplex data with totalseq B antibodies using hashsolo?
cellranger. seq hashsolo rna
17 months ago by bioinfo ▴ 150
0
votes
2
replies
758
views
Do I need to specify the introns on the gtf file for cellranger?
fasta gtf cellranger scRNAseq
updated 18 months ago by 146k • written 18 months ago by ▴ 150
3
votes
1
reply
741
views
Can I normalize several samples with DESeq2 and then do pairwise comparisons?
deseq2 rna-seq
updated 18 months ago by 13k • written 18 months ago by ▴ 150
1
vote
1
reply
680
views
Do indexes made with cDNA fasta file contain only mRNAs?
ensembl kallisto
updated 19 months ago by ★ 6.9k • written 19 months ago by ▴ 150
0
votes
0
replies
429
views
How to analyze SCRNA seq data labelled with LARRY?
single lineage RNA tracing LARRY
updated 19 months ago by 146k • written 19 months ago by ▴ 150
2
votes
5
replies
1.7k
views
How to add gene entry to gtf file?
single-cell cellranger
updated 19 months ago by 44k • written 19 months ago by ▴ 150
2
votes
5
replies
1.3k
views
Problem with tximport and plasmodium falciparum
tximport
19 months ago by bioinfo ▴ 150
1
vote
3
replies
2.5k
views
How to make a UMAP for single cell data and color cells by average expression of a list of genes in scanpy?
single-cell scanpy RNA-seq UMAP
19 months ago by bioinfo ▴ 150
1
vote
5
replies
1.4k
views
How to interpret dotplot from enrichment analysis with gseapy?
gsea single-cell gseapy enrichR
19 months ago by bioinfo ▴ 150
3
votes
4
replies
980
views
How to remove a gene before making a cellranger reference?
fasta gtf cellranger scRNAseq
updated 20 months ago by 85k • written 20 months ago by ▴ 150
1
vote
2
replies
593
views
Do I need to merge files after downloading them from SRA?
rna-seq sra
20 months ago by bioinfo ▴ 150
15
votes
8
replies
5.8k
views
Encountering error when loading scanpy?
scanpy single-cell scRNA-seq
19 months ago by bioinfo ▴ 150
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