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When should I normalize and subset adata objects in scanpy?
scanpy scRNA-seq single-cell
updated 22 days ago by 4.2k • written 22 days ago by ▴ 150
0
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1
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232
views
How to choose cells that co-express several genes with scanpy?
scanpy scRNA-seq single-cell
updated 5 weeks ago by 4.2k • written 5 weeks ago by ▴ 150
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0
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143
views
How to run trajectory analysis with only one cell type using palantir?
palantir scanpy
7 weeks ago by bioinfo ▴ 150
2
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1
reply
217
views
Do I need to remove doublets after before or after running hashsolo?
hashsolo scanpy scrublet
updated 7 weeks ago by ▴ 890 • written 7 weeks ago by ▴ 150
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0
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240
views
Comment: Comment: How can I import an unindexed human gtf file in IGV?
8 weeks ago by bioinfo ▴ 150
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2
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240
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How can I import an unindexed human gtf file in IGV?
igv
8 weeks ago by bioinfo ▴ 150
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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
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1
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521
views
Comment: Comment: Why am I getting such a big difference in alignment rates in kallisto?
11 weeks ago by bioinfo ▴ 150
0
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1
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521
views
Comment: Comment: Why am I getting such a big difference in alignment rates in kallisto?
11 weeks ago by bioinfo ▴ 150
0
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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
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1
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348
views
Comment: Comment: Where are the illumina adapters on Trimmomatic take from?
3 months ago by bioinfo ▴ 150
1
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3
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348
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Where are the illumina adapters on Trimmomatic take from?
rna-seq trimmomatic
updated 3 months ago by 145k • written 3 months ago by ▴ 150
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0
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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
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2
replies
402
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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
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1
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839
views
Comment: Comment: How should I make kallisto indexes?
4 months ago by bioinfo ▴ 150
1
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5
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839
views
How should I make kallisto indexes?
kallisto
updated 4 months ago by ★ 6.8k • written 4 months ago by ▴ 150
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0
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406
views
Comment: Comment: Can I compare kallisto counts from samples with different amount of reads?
4 months ago by bioinfo ▴ 150
0
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0
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463
views
Comment: Comment: How to row normalize a matrixplot?
4 months ago by bioinfo ▴ 150
1
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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
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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 44k • written 4 months ago by ▴ 150
0
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0
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475
views
Comment: Comment: How to compare bulk RNA seq data demultiplexed in different ways?
5 months ago by bioinfo ▴ 150
0
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1
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475
views
Comment: Comment: How to compare bulk RNA seq data demultiplexed in different ways?
5 months ago by bioinfo ▴ 150
0
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5
replies
475
views
How to compare bulk RNA seq data demultiplexed in different ways?
RNA-seq
updated 4 months ago by 44k • written 5 months ago by ▴ 150
0
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1
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791
views
Comment: Comment: How does kallisto handle multi mapped reads?
6 months ago by bioinfo ▴ 150
0
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1
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791
views
Comment: Comment: How does kallisto handle multi mapped reads?
6 months ago by bioinfo ▴ 150
3
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7
replies
791
views
How does kallisto handle multi mapped reads?
kallisto
updated 6 months ago by ★ 6.8k • written 6 months ago by ▴ 150
0
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2
replies
550
views
How to add motifs in cellranger-arc reference?
gtf scRNAseq fasta cellranger
updated 4 months ago by • 0 • written 6 months ago by ▴ 150
0
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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 20k • written 9 months ago by ▴ 150
0
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1
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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
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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
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1
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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 44k • written 9 months ago by ▴ 150
0
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0
replies
860
views
Comment: Comment: Why am I getting different results with kallisto?
9 months ago by bioinfo ▴ 150
0
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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
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1
reply
656
views
Comment: Comment: Are truseq adapter sequences picked up by FASTQC?
9 months ago by bioinfo ▴ 150
2
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3
replies
656
views
Are truseq adapter sequences picked up by FASTQC?
fastqc truseq
updated 9 months ago by 145k • written 9 months ago by ▴ 150
0
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0
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424
views
How to convert dataframe properly to anndata?
single-cell python anndata
updated 4 months ago by 44k • written 10 months ago by ▴ 150
0
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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 44k • written 10 months ago by ▴ 150
0
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0
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385
views
How to subsample ATAC fragment file?
single-cell atac-seq scRNA-seq
updated 4 months ago by 44k • written 10 months ago by ▴ 150
0
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0
replies
872
views
Comment: Comment: How to assign gene names after kallisto when I add GFP?
10 months ago by bioinfo ▴ 150
0
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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 ★ 28k • written 10 months ago by ▴ 150
1
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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
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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
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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
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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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