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How to use lme4() to perform differential expression on bulk RNA seq data with multiple random effects?
bulkRNAseq lme4
updated 3 months ago by 86k • written 3 months ago by ▴ 20
0
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1
reply
449
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Downloading the raw microarray data from GEO
.gpr microarray .CEL
updated 9 months ago by 148k • written 9 months ago by ▴ 20
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0
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4.3k
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Comment: Comment: Tutorial for analysing gpr files of microarray
10 months ago by bioyas ▴ 20
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0
replies
754
views
Integration of scatac-seq data with another integrated scRNA and scATAC data set
Signac integration scATAC Seurat scRNA
2.0 years ago by bioyas ▴ 20
1
vote
1
reply
767
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separate read1 and read2 from merged fastq file and align against reference genome
fastq alignment regex headers
updated 2.2 years ago by 11k • written 2.2 years ago by ▴ 20
0
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0
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758
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Comment: Comment: different pileups between sorted.bam file and bigwig file
2.7 years ago by bioyas ▴ 20
0
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1
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2.5k
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Comment: Comment: Loading possorted_genome_bam.bam generated by 10X cellranger count command into
2.7 years ago by bioyas ▴ 20
0
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2
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758
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different pileups between sorted.bam file and bigwig file
bigwig deeptools IGV
updated 19 months ago by 44k • written 2.7 years ago by ▴ 20
0
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1
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2.5k
views
Comment: Comment: Loading possorted_genome_bam.bam generated by 10X cellranger count command into
2.7 years ago by bioyas ▴ 20
3
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5
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2.5k
views
Loading possorted_genome_bam.bam generated by 10X cellranger count command into IGV.
cellranger deeptools bigwig IGV single-cell
updated 19 months ago by 44k • written 2.7 years ago by ▴ 20
1
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2
replies
2.9k
views
quantify counts from sorted bam files using a bed file containing regions of interest
counts featureCount bam Bed
updated 2.9 years ago by ★ 1.5k • written 2.9 years ago by ▴ 20
0
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1
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9.4k
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Comment: Comment: filter out fasta File by pattern
2.9 years ago by bioyas ▴ 20
3
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4
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1.6k
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Convert per base bedgraph to Bed format
Bedgraph perbase Bed Bedtools
updated 3.8 years ago by 36k • written 3.8 years ago by ▴ 20
0
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0
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2.0k
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Comment: C: How to Identify Housekeeping genes from gene expression matrix and normalize the
4.3 years ago by bioyas ▴ 20
0
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1
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2.0k
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Comment: C: How to Identify Housekeeping genes from gene expression matrix and normalize the
4.3 years ago by bioyas ▴ 20
0
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1
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2.0k
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Comment: C: How to Identify Housekeeping genes from gene expression matrix and normalize the
4.3 years ago by bioyas ▴ 20
1
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6
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2.0k
views
How to Identify Housekeeping genes from gene expression matrix and normalize the data
housekeeping genes normalization R edger limma
4.3 years ago by bioyas ▴ 20
0
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0
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1.5k
views
Comment: C: Differential Expression analysis between single cell RNa seq & bulk RNa seq data
4.5 years ago by bioyas ▴ 20
1
vote
3
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1.5k
views
Differential Expression analysis between single cell RNa seq & bulk RNa seq data
rna-seq Bulk rna seq DE analysis SC-RNA-sq
updated 4.5 years ago by 14k • written 4.5 years ago by ▴ 20
0
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1
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34k
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Comment: C: Can the code of a R package be changed? How?
4.7 years ago by bioyas ▴ 20
5
votes
5
replies
4.2k
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DEG analysis between 2 samples using edger
edger RNA-Seq biological_replicates
updated 4.7 years ago by ★ 7.8k • written 4.7 years ago by ▴ 20
0
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1
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4.2k
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Comment: C: DEG analysis between 2 samples using edger
4.7 years ago by bioyas ▴ 20
0
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0
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1.7k
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Comment: C: getting 0 counts using hisat2 and feature_count pipeline
5.0 years ago by bioyas ▴ 20
0
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1
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1.7k
views
Comment: C: getting 0 counts using hisat2 and feature_count pipeline
5.0 years ago by bioyas ▴ 20
3
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4
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1.7k
views
getting 0 counts using hisat2 and feature_count pipeline
RNA-Seq Hisat2 featurecounts count
updated 5.0 years ago by 14k • written 5.0 years ago by ▴ 20
3
votes
4
replies
6.5k
views
How to get the gene expression matrix from GEO while getGEO returns 0 features?
GETquery ATAC-seq GEO getGEO RNA-Seq
updated 19 months ago by 44k • written 5.5 years ago by ▴ 20
0
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1
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6.5k
views
Comment: C: How to get the gene expression matrix from GEO while getGEO returns 0 features?
5.5 years ago by bioyas ▴ 20
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