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scVI vs Harmony, which is better for cell type based clustering in brain tissue?
harmony scVI single cell
updated 4 weeks ago by 90k • written 5 weeks ago by ▴ 110
0
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1
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12k
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Comment: Comment: Regarding the usage of raw vs filtered bc matrices
8 weeks ago by biotrekker ▴ 110
0
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1
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12k
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Comment: Comment: Regarding the usage of raw vs filtered bc matrices
8 weeks ago by biotrekker ▴ 110
0
votes
1
reply
12k
views
Comment: Comment: Regarding the usage of raw vs filtered bc matrices
8 weeks ago by biotrekker ▴ 110
0
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0
replies
12k
views
Comment: Comment: Regarding the usage of raw vs filtered bc matrices
8 weeks ago by biotrekker ▴ 110
8
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11
replies
12k
views
Regarding the usage of raw vs filtered bc matrices
10X ranger cell snRNAseq
updated 8 weeks ago by ★ 7.8k • written 9 weeks ago by ▴ 110
0
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2
replies
788
views
Merge Seurat objects
seurat merge single-cell
updated 8 months ago by 45k • written 9 months ago by ▴ 110
0
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1
reply
732
views
How do I use msigdb to annotate the single cell data?
msigdb single-cell
updated 15 months ago by 45k • written 16 months ago by ▴ 110
0
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0
replies
951
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Comment: Comment: single nucleus RNA seq processing pipeline questions
16 months ago by biotrekker ▴ 110
2
votes
1
reply
788
views
I am getting an error with Kallisto Bustools wrapper (kb) command to create an index
kb kallisto bustools
updated 16 months ago by ★ 7.8k • written 16 months ago by ▴ 110
0
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0
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1.1k
views
Comment: Comment: Is the 10X multiome chemistry most similar similar to 10XV1, 10XV2, or 10XV3?
16 months ago by biotrekker ▴ 110
2
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2
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1.1k
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Is the 10X multiome chemistry most similar similar to 10XV1, 10XV2, or 10XV3?
snRNAseq kallisto 10X
16 months ago by biotrekker ▴ 110
1
vote
2
replies
951
views
single nucleus RNA seq processing pipeline questions
demultiplexing snRNAseq
16 months ago by biotrekker ▴ 110
0
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1
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1.1k
views
Comment: Comment: Can I go from kallisto results to SEURAT directly
17 months ago by biotrekker ▴ 110
1
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3
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1.1k
views
Can I go from kallisto results to SEURAT directly
cell bustoolls kallisto single
updated 17 months ago by ★ 7.8k • written 17 months ago by ▴ 110
0
votes
1
reply
669
views
How do I run fastq-dump on multiple prefetched files at once?
sratoolkit fastq-dump
updated 19 months ago by 166k • written 19 months ago by ▴ 110
2
votes
4
replies
1.3k
views
How to I use prefetch (SRAtoolkit) on multiple accessions all at one?
sratoolkit prefetch
updated 19 months ago by 166k • written 19 months ago by ▴ 110
0
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1
reply
1.3k
views
Comment: Comment: Is there a reason why fastq files from SRAExplorer and SRAToolkit are different
20 months ago by biotrekker ▴ 110
0
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1
reply
1.3k
views
Comment: Comment: Is there a reason why fastq files from SRAExplorer and SRAToolkit are different
20 months ago by biotrekker ▴ 110
1
vote
5
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1.3k
views
Is there a reason why fastq files from SRAExplorer and SRAToolkit are different sizes?
sraexplorer sratoolkit
updated 20 months ago by 154k • written 20 months ago by ▴ 110
0
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0
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2.4k
views
Comment: Comment: How do I use md5sum to check if my .fastq files from SRA Explorer have been down
20 months ago by biotrekker ▴ 110
0
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2
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2.4k
views
Comment: Comment: How do I use md5sum to check if my .fastq files from SRA Explorer have been down
20 months ago by biotrekker ▴ 110
2
votes
7
replies
2.4k
views
How do I use md5sum to check if my .fastq files from SRA Explorer have been downloaded correctly
scRNA-seq md5
updated 9 months ago by 90k • written 21 months ago by ▴ 110
0
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0
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2.0k
views
Comment: Comment: Error with fastq file corruption when downloading from SRA explorer using SLURM
22 months ago by biotrekker ▴ 110
2
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6
replies
2.0k
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Error with fastq file corruption when downloading from SRA explorer using SLURM job
SRAExplorer corruption rna-seq SLURM
22 months ago by biotrekker ▴ 110
4
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4
replies
1.7k
views
How to combine different "groups" in DESeq2 constrast
rnaseq DESeq2
updated 2.7 years ago by 15k • written 2.7 years ago by ▴ 110
0
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1
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1.7k
views
Comment: Comment: How to combine different "groups" in DESeq2 constrast
2.7 years ago by biotrekker ▴ 110
7
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1
reply
2.0k
views
How to use filterbyExpr with DESeq2?
DESeq2 RNA-seq edgeR
updated 2.7 years ago by 45k • written 2.7 years ago by ▴ 110
5
votes
2
replies
2.5k
views
How do I go from TPM to PCA (rna-seq)?
pca rnaseq tpm
updated 2.8 years ago by 90k • written 2.8 years ago by ▴ 110
0
votes
1
reply
832
views
How do I use tximport to annotate using ensemble annotation on GRCh37.75?
tximport ensemble annotation
updated 2.8 years ago by 90k • written 2.8 years ago by ▴ 110
0
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1
reply
1.4k
views
What is the best way to process a metadata file that SEURAT can read?
metadata scRNAseq seurat
updated 3.2 years ago by ★ 1.8k • written 3.2 years ago by ▴ 110
1
vote
1
reply
4.3k
views
Comment: Comment: Analyzing single cell RNA seq with multiple samples and conditions
3.2 years ago by biotrekker ▴ 110
12
votes
3
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4.3k
views
Analyzing single cell RNA seq with multiple samples and conditions
cell merge single seurat scRNAseq
3.2 years ago by biotrekker ▴ 110
1
vote
1
reply
1.7k
views
Need some help with next steps after getting fGSEA results from Microarray data.
microarray differential expression analysis fGSEA
updated 4.3 years ago by ▴ 20 • written 5.1 years ago by ▴ 110
47
votes
24
replies
7.9k
views
13 follow
Forum: What programming language do you use the most in your work? Which one do you like the best?
Programming Python R Scripting
updated 2.7 years ago by 45k • written 4.8 years ago by ▴ 110
0
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0
replies
1.0k
views
I am having trouble running tmodhg with ECC library?
tmodhg microarray analysis
updated 5.0 years ago by 21k • written 5.0 years ago by ▴ 110
1
vote
2
replies
1.5k
views
I am having trouble downloading msigdb_v7.2.xml
msigdb
updated 5.0 years ago by 154k • written 5.0 years ago by ▴ 110
0
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0
replies
1.5k
views
Comment: C: I am having trouble downloading msigdb_v7.2.xml
5.0 years ago by biotrekker ▴ 110
1
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1
reply
4.9k
views
Answer: A: Getting error when using lmfit (LIMMA) for Microarray data analysis
5.2 years ago by biotrekker ▴ 110
4
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23
replies
4.9k
views
Getting error when using lmfit (LIMMA) for Microarray data analysis
R Microarray LIMMA
5.2 years ago by biotrekker ▴ 110
0
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1
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4.9k
views
Comment: C: Getting error when using lmfit (LIMMA) for Microarray data analysis
updated 5.2 years ago by 90k • written 5.2 years ago by ▴ 110
0
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2
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4.9k
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Comment: C: Getting error when using lmfit (LIMMA) for Microarray data analysis
5.2 years ago by biotrekker ▴ 110
0
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1
reply
4.9k
views
Comment: C: Getting error when using lmfit (LIMMA) for Microarray data analysis
5.2 years ago by biotrekker ▴ 110
0
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1
reply
4.9k
views
Comment: C: Getting error when using lmfit (LIMMA) for Microarray data analysis
5.2 years ago by biotrekker ▴ 110
0
votes
1
reply
4.9k
views
Comment: C: Getting error when using lmfit (LIMMA) for Microarray data analysis
updated 5.2 years ago by 90k • written 5.2 years ago by ▴ 110
0
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1
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4.9k
views
Comment: C: Getting error when using lmfit (LIMMA) for Microarray data analysis
updated 5.2 years ago by 90k • written 5.2 years ago by ▴ 110
0
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1
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4.9k
views
Comment: C: Getting error when using lmfit (LIMMA) for Microarray data analysis
updated 5.2 years ago by 90k • written 5.2 years ago by ▴ 110
0
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1
reply
4.9k
views
Comment: C: Getting error when using lmfit (LIMMA) for Microarray data analysis
5.2 years ago by biotrekker ▴ 110
0
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1
reply
4.9k
views
Comment: C: Getting error when using lmfit (LIMMA) for Microarray data analysis
updated 5.2 years ago by 90k • written 5.2 years ago by ▴ 110
0
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1
reply
2.7k
views
Comment: C: Cannot get read.celfiles() method to work?
5.3 years ago by biotrekker ▴ 110
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