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0
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1
reply
1.6k
views
positive and negative Fold Change glmLRT test
RNA-Seq log2FC glmLRT differential-expression
updated 11 weeks ago by 43k • written 5.0 years ago by ▴ 260
21
votes
18
replies
22k
views
9 follow
Cleaning RNA-Seq data from rRNA
RNA-Seq rRNA cleaning QC
updated 23 months ago by ▴ 40 • written 8.1 years ago by ▴ 260
0
votes
2
replies
879
views
Conserved regions in multiple fasta files (multiple species)?
fasta ClustalW Alignment
updated 13 months ago by 43k • written 2.4 years ago by ▴ 260
0
votes
2
replies
4.6k
views
How to calculate the AUC value for a ranger RF model ?
AUC value ranger randomForest classification
updated 2.7 years ago by • 0 • written 6.7 years ago by ▴ 260
3
votes
3
replies
864
views
from fasta to gtf format?
gtf DE fasta
updated 3 months ago by ▴ 200 • written 3.0 years ago by ▴ 260
1
vote
3
replies
1.1k
views
different read names in paired-end data
fastq file read name header ABI-Solid
updated 3.1 years ago by 13k • written 3.1 years ago by ▴ 260
0
votes
3
replies
1.2k
views
prefetch and fast-dump problems?
prefetch SRA fastq-dump
updated 13 months ago by 43k • written 3.2 years ago by ▴ 260
0
votes
0
replies
580
views
tophat2 mapping fr-firststrand or fr-secondstrand ?
tophat2 fr-firststrand fr-secondstrand AB SOLiD
3.1 years ago by debitboro ▴ 260
0
votes
0
replies
794
views
cuffmerge gtf_to_sam error?
assembly cufflinks cuffmerge gtf_to_sam
3.1 years ago by debitboro ▴ 260
0
votes
0
replies
2.3k
views
How to get the normalized counts matrix EDASeq ?
RNA-Seq normalization within lane normalization
updated 3.3 years ago by ▴ 140 • written 7.1 years ago by ▴ 260
0
votes
0
replies
423
views
How can I adjust the Age of sample population?
age adjustment direct standardization
3.9 years ago by debitboro ▴ 260
4
votes
8
replies
2.9k
views
How to append two fastq files ?
fastq RNA-Seq append merge
updated 20 months ago by ▴ 20 • written 4.4 years ago by ▴ 260
0
votes
1
reply
1.6k
views
sortMeRNA before or after adapters trimming ?
RNA-Seq rRNA sortMeRNA
updated 5.8 years ago by ★ 1.9k • written 6.0 years ago by ▴ 260
1
vote
9
replies
3.2k
views
All my reads fall in intergenic regions ?
RNA-Seq count per biotype intergenic regions
updated 6.0 years ago by 8.9k • written 6.0 years ago by ▴ 260
0
votes
1
reply
4.0k
views
Questions about STAR and Bowtie (not Bowtie2) mapping
RNA-Seq STAR Bowtie uniquely mapped reads
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 260
2
votes
12
replies
4.0k
views
short RNA reads alignment
RNA-Seq short reads alignment
6.0 years ago by debitboro ▴ 260
0
votes
1
reply
979
views
Check variance stabilization transformation ?
RNA-Seq variance stabilization DESeq2
updated 6.1 years ago by 14k • written 6.1 years ago by ▴ 260
0
votes
2
replies
2.4k
views
WGNCA RNASeq without time series
time-series RNA-Seq WGCNA
updated 11 months ago by 43k • written 8.0 years ago by ▴ 260
0
votes
0
replies
1.4k
views
How can I get the OOB samples used for each tree in random forest model R?
randomForest OOB samples
6.4 years ago by debitboro ▴ 260
4
votes
3
replies
4.6k
views
Technical and Biological replicates
RNA-Seq technical replicates biological replicates
updated 6.4 years ago by ▴ 30 • written 8.0 years ago by ▴ 260
2
votes
1
reply
2.0k
views
ggplot expression values as function of samples and classes
ggplot miRNA expression classes
updated 6.7 years ago by 5.2k • written 6.7 years ago by ▴ 260
0
votes
8
replies
2.4k
views
Tophat2 mapping takes a lot of time
Tophat2 mapping Cluster
updated 6.9 years ago by 20 • written 8.0 years ago by ▴ 260
0
votes
0
replies
1.9k
views
ConsensusPathDB pathway enrichment analysis
Enrichemnt analysis ConsensusPathDB
6.9 years ago by debitboro ▴ 260
0
votes
1
reply
1.7k
views
How can I check for library composition bias RNA-seq data
library composition bias normalization RNA-seq
updated 6.9 years ago by ★ 1.7k • written 6.9 years ago by ▴ 260
2
votes
5
replies
3.6k
views
I get the same modules but different number of genes WGCNA
WGCNA Module genes geneModuleMembership
7.0 years ago by debitboro ▴ 260
0
votes
0
replies
1.7k
views
OOB error vs Cross Validation
random Forests Cross validation OOB error
7.0 years ago by debitboro ▴ 260
1
vote
2
replies
1.9k
views
positive control and negative control genes list
positive control genes DEGs
7.1 years ago by debitboro ▴ 260
1
vote
1
reply
6.1k
views
How can I get the normalized counts matrix after doing TMM normalization using edgeR
TMM CPM normalization
updated 7.1 years ago by ▴ 70 • written 7.3 years ago by ▴ 260
3
votes
2
replies
4.5k
views
Correct for GC content bias RNASeq DE
RNA-Seq GC content Normalization
updated 7.1 years ago by 6.5k • written 7.1 years ago by ▴ 260
0
votes
1
reply
2.4k
views
download gene expression data
gene-expression
updated 13 months ago by 43k • written 7.2 years ago by ▴ 260
0
votes
1
reply
1.8k
views
filtering or not the gtf annotation file from ncRNA, tRNA, and rRNA before mapping ?
RNA-Seq
updated 13 months ago by 43k • written 7.2 years ago by ▴ 260
0
votes
1
reply
1.3k
views
How to get SNP data, DNA methylation, and proteomic data ?
SNP data DNA Methylation data proteomic data
7.3 years ago by debitboro ▴ 260
0
votes
1
reply
2.3k
views
How to get the normalized counts matrix
normalization EDASeq UQ
7.3 years ago by debitboro ▴ 260
4
votes
7
replies
3.6k
views
Using of WGCNA to identify modules in Normal/Tumor tissues
WGCNA module-trait correlation NA value
updated 7.4 years ago by 20 • written 7.5 years ago by ▴ 260
7
votes
4
replies
7.8k
views
Differences between co-expression and co-regulation
co-expression co-regulation
updated 7.4 years ago by ★ 1.2k • written 7.4 years ago by ▴ 260
5
votes
6
replies
4.8k
views
WGCNA heatmap modules-trait relationship
WGCNA heatmap modules-trait relationship
7.5 years ago by debitboro ▴ 260
0
votes
2
replies
3.1k
views
How can I get the gene annotation file from Illumina (RNA Sequencing) ?
RNA-Seq Gene annotation file illumina
updated 7.7 years ago by 8.7k • written 7.7 years ago by ▴ 260
0
votes
3
replies
5.2k
views
Gene length table from gtf file for rpkm() function
gene length HTSeq count RPKM edgeR
updated 20 months ago by 7.5k • written 7.8 years ago by ▴ 260
1
vote
2
replies
1.4k
views
Check if RNASeq count data follow NB or Poisson distributions
RNA-Seq Negative Binomial Poisson distribution
updated 7.9 years ago by 104k • written 7.9 years ago by ▴ 260
1
vote
2
replies
2.2k
views
RNASeq DE analysis between tumor and normal tissues
RNA-Seq DE analysis HTSeq-count DESeq2
7.9 years ago by debitboro ▴ 260
1
vote
2
replies
2.3k
views
Cufflinks: exceeded memory limit (31836604 > 31457280), being killed
Cufflinks memory limit slurm
7.9 years ago by debitboro ▴ 260
1
vote
1
reply
2.4k
views
Memory and Runtime Cufflinks
cufflinks runtime tophat2
7.9 years ago by debitboro ▴ 260
1
vote
3
replies
2.4k
views
Splitting fastq file for mapping with tophat2
RNA-Seq tophat2 fatsq files splitting
updated 8.0 years ago by ★ 1.4k • written 8.0 years ago by ▴ 260
2
votes
5
replies
4.3k
views
Indexing human reference genome before STAR Mapping
STAR Indexing Error Mapping
8.0 years ago by debitboro ▴ 260
0
votes
0
replies
1.8k
views
Tophat2 error when mapping using -G option
RNA-Seq tophat2 mapping with -G option
8.0 years ago by debitboro ▴ 260
3
votes
2
replies
1.7k
views
select chr22 lines from Ensembl GTF file
gtf files chr22.gtf RNA-Seq Ensembl
updated 8.0 years ago by 23k • written 8.0 years ago by ▴ 260
0
votes
4
replies
1.8k
views
Tophat2 error when mapping a sample file to a reference
rna-seq seqtk sampling
8.0 years ago by debitboro ▴ 260
13
votes
14
replies
4.7k
views
8 follow
RNA-Seq for DE analysis
RNA-Seq Differential Expression Analysis
updated 8.0 years ago by ★ 2.4k • written 8.1 years ago by ▴ 260
1
vote
1
reply
2.6k
views
RNA-Seq Mapping and bowtie2 indexing
RNA-Seq Mapping Bowtie2 indexing
8.0 years ago by debitboro ▴ 260
20
votes
12
replies
11k
views
Fastqc for RNA-Seq data (Illumina 1.9)
RNA-Seq Fastqc Kmer content
updated 8.1 years ago by 54k • written 8.1 years ago by ▴ 260
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