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Showing top results for tag: RNA-seq • reset
1
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107
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Using NumReads column of quants.genes.sf file to build DESeq2 input
R deseq2 rna-seq salmon
updated 16 hours ago by 20k • written 17 hours ago by ▴ 10
0
votes
0
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95
views
PyDeseq2 - InvalidIndexError
python rna-seq pandas pydeseq2 deseq2
1 day ago by tmanjonas • 0
1
vote
3
replies
819
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Error in CIBERSORTx ($ operator is invalid for atomic vectors)
RNA-Seq CIBERSORTx deconvolution cibersort
updated 1 day ago by • 0 • written 8 months ago by ▴ 10
1
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12
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5.4k
views
7 follow
Error in CIBERSORTx
RNA-seq CIBERSORT LM22
updated 1 day ago by • 0 • written 2.1 years ago by • 0
2
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6
replies
2.4k
views
Question: can not obtain DESeq2 results
RNA-Seq DESeq2
updated 2 days ago by ▴ 10 • written 4.3 years ago by ▴ 10
0
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0
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113
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CIBERSORTx error (error in rep(2, size * length(cells) -1)) : invalid 'times' argument
CIBERSORTx CIBERSORT scRNA-seq RNA-seq Deconvolution
2 days ago by Amairani • 0
0
votes
3
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316
views
merge my own RNA-seq data with TCGA UCSCXena data sets. and proper normalisation
Xena TCGA normalisation RNA-seq
7 days ago by theodore ▴ 90
0
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0
replies
151
views
immunedeconv for RNAseq data
meta-analysis rna-seq immunedeconv deseq2
8 days ago by a.stef.44 ▴ 10
3
votes
2
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240
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RNA-seq heatmaps: effective length, RPKM vs. CPM
edgeR RNA-seq
updated 9 days ago by 85k • written 9 days ago by ▴ 40
1
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4
replies
328
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Bulk RNA seq PCA plot issues
RNA-seq PCA
updated 10 days ago by 44k • written 10 days ago by • 0
0
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0
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150
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News: Upcoming November Courses – Enhance Your Skills in Bioinformatics and Data Analysis
Population-Genomics scRNA-seq RNA-seq Metagenomics Genome-Assembly
10 days ago by carlopecoraro2 ★ 2.6k
0
votes
1
reply
955
views
Using TCGABioLinks to query multiple cancer studies
RNA-Seq R TCGA
updated 10 days ago by 146k • written 3.8 years ago by • 0
0
votes
1
reply
315
views
News: Online Workshop - Bioinformatics Pipeline Development with Nextflow (November 13-15, 2024)
Workshop Nextflow RNA-Seq
10 days ago by ecSeq Bioinformatics • 0
1
vote
1
reply
197
views
Raw reads or raw counts for meta-analysis
meta-analysis rna-seq HTSEQ STAR
updated 10 days ago by 44k • written 11 days ago by ▴ 10
0
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0
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135
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Need help with providing RNA Seq data to run braker.pl in ETP mode.
augustus gene-prediction rna-seq braker genemark
11 days ago by Vijith ▴ 60
2
votes
0
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144
views
Blog: How Seurat PCA projection, KNN and MNN for label transfer work
R RNA-seq scRNA-seq PCA
updated 10 days ago by 44k • written 11 days ago by ★ 4.4k
0
votes
1
reply
155
views
Mitochondrial Transcriptome Analysis with PacBio RNA Data using Geneious Prime
NGS RNA-seq PacBio
updated 14 days ago by 44k • written 15 days ago by ▴ 40
0
votes
8
replies
658
views
Question on batch effect for a bulk RNA seq analysis
RNA-seq batch-effect
15 days ago by akb • 0
2
votes
1
reply
428
views
Feature Counts: low assigned alignments (1.9%) with -s 0: Unstranded option any assigned alignments with -s 2: reversely strandedoptionts
alignments RNA-seq
updated 15 days ago by 44k • written 15 days ago by • 0
2
votes
2
replies
298
views
Outlier after DEseq2 in meta-analysis
meta-analysis rna-seq outlier DESeq2
16 days ago by a.stef.44 ▴ 10
1
vote
2
replies
361
views
Questions Regarding Normalization and Standardization in RNA-seq Differential Analysis
RNA-seq Normalization
updated 20 days ago by 44k • written 21 days ago by ▴ 10
0
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0
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199
views
News: Online Workshop - A Practical Introduction to NGS Data Analysis (December 9-11, 2024)
Workshop Variant-Calling RNA-Seq Illumina DNA-Seq
updated 20 days ago by 44k • written 20 days ago by • 0
0
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2
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345
views
extracting reads from FASTA/FASTQ file
RNA-seq RNA
updated 21 days ago by 146k • written 21 days ago by • 0
0
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3
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385
views
Different annotations for different isoforms from the same gene
metatranscriptomics Trinity RNA-seq Isoform
updated 20 days ago by ★ 2.7k • written 21 days ago by • 0
0
votes
1
reply
262
views
DeSeq2 filter transcripts
DeSeq2 RNA-seq RNA
updated 21 days ago by 11k • written 21 days ago by • 0
1
vote
2
replies
339
views
DESeq2: adjusted p-values become NA when sub-setting samples
R DEG RNA-seq DESeq2
updated 21 days ago by 146k • written 21 days ago by ▴ 190
2
votes
6
replies
650
views
WGCNA package.
RNA-seq WGCNA
20 days ago by Jaber ▴ 30
0
votes
1
reply
239
views
Getting data from NCBI using Python
Ensembl pyEnsembl RNA-seq
updated 21 days ago by 44k • written 22 days ago by • 0
0
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0
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209
views
News: Course - RNA Sequencing Data with R/Bioconductor
R Bioconductor RNA-seq Differential-Expression-Analysis
updated 26 days ago by 44k • written 27 days ago by ★ 2.6k
1
vote
0
replies
220
views
Inflammatory genes identification
Cancer inflammatory-genes RNA-Seq
updated 27 days ago by 44k • written 27 days ago by ▴ 30
1
vote
1
reply
281
views
only ~12% of assigned reads on featurecount
RNA-seq
updated 28 days ago by ▴ 290 • written 28 days ago by ▴ 20
2
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5
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1.6k
views
UMItools dedup deduplication taking too much time + RAM
UMI-tools bam RNA-seq
updated 27 days ago by 20k • written 2.8 years ago by ▴ 20
0
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0
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192
views
Salmon transcript-level to gene-level quantification
R Salmon RNA-Seq
28 days ago by Mitmischer • 0
0
votes
1
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222
views
filter genes for differential gene expression
RNA-seq differential-gene-expression
updated 29 days ago by 44k • written 29 days ago by • 0
6
votes
6
replies
455
views
RNA-Seq multiple lane
bam RNA-seq transcriptomics
28 days ago by MaxMin ▴ 10
2
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3
replies
345
views
Error during batch correction/PCA
RNA-seq batch-effect
29 days ago by Eduardo Oñate • 0
0
votes
8
replies
565
views
HTseq count issue, not aligning to features
htseq hisat2 rna-seq
27 days ago by boone5jones • 0
4
votes
13
replies
810
views
6 follow
featureCounts segmentation fault
featureCounts pipeline RNA-Seq
29 days ago by Jaber ▴ 30
7
votes
8
replies
583
views
Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, and intron only
rna-seq featurecounts
4 weeks ago by Ian 6.1k
1
vote
1
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261
views
Visualizing Upregulated and Downregulated Genes in GO and KEGG Pathway Analyses
RNA-Seq
updated 4 weeks ago by ▴ 100 • written 4 weeks ago by ▴ 10
0
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0
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176
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Issues with EnrichPathway Barplot in Reactome Pathway Analysis
RNA-Seq
4 weeks ago by roxana ▴ 10
3
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6
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646
views
FastQC and HISAT2
HISAT2 FastQC RNA-Seq
updated 4 weeks ago by 146k • written 5 weeks ago by ▴ 30
0
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0
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159
views
News: An Introduction to Nanopore direct RNA sequencing
cDNA RNA-seq Nanopore
updated 4 weeks ago by 44k • written 4 weeks ago by ★ 2.6k
3
votes
2
replies
319
views
Numreads from samtools for Differential Expression
samtools featurecounts rna-seq deseq numreads
updated 4 weeks ago by 44k • written 4 weeks ago by • 0
2
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3
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431
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Choosing the Best Method for DEG Analysis: limma vs. DESeq2 for RSEM Normalized RNA-Seq Data
dese2 cbioportal RNA-seq limma
updated 4 weeks ago by 101k • written 4 weeks ago by ▴ 140
0
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0
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197
views
Bandage visualization of the transcriptome
Trinity transcriptomics Bandage RNA-seq
updated 4 weeks ago by 44k • written 4 weeks ago by ▴ 30
7
votes
12
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941
views
RNA-Seq mutation calling without germline data
rna-seq mutation
updated 1 day ago by 4.0k • written 5 weeks ago by • 0
1
vote
4
replies
396
views
Poor dispersion fit in DESeq2
deseq2 RNA-seq edgeR limma
updated 5 weeks ago by 44k • written 5 weeks ago by ▴ 20
1
vote
5
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446
views
RNASeq Analysis: data from different library
RNA-seq ngs
updated 5 weeks ago by 20k • written 5 weeks ago by • 0
2
votes
1
reply
286
views
ROAST
RNA-SEQ
updated 5 weeks ago by 146k • written 5 weeks ago by ▴ 110
50 results • Page 1 of 1
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Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How? by ATpoint 85k
> But How could I know if the difference comes from sample instead of sequencing runs or cohort-driven batch effect? You cannot. It's pe…
Comment: Comparing GSEA mutant data to wild type by conmul • 0
Sorry that it was unclear in the post. The data is all CRISPR gene effect scores from DepMap. The 'significant genes' as mentioned in the p…
Comment: How to determine whether it is 10x data by king • 0
Thank you for your answer, it's very inspiring.
Comment: Inquiry about depth of coverage and copy number variation by Chen • 0
Thanks Pierre, I was actually thinking about the duplicate PCR reads and didn't explain it properly. I have found a post mentioning that qu…
Comment: Can a read be aligned more than once? by GenoMax 146k
Yes a read can be aligned more than once (I don't specifically know about gam/gaf). It would be called a "multi-mapping" read. You could im…
Comment: Statistical test to be used for dataset by allingt • 0
The choice of test depends on the types of variables involved and the hypothesis you have. But most importantly on the question you want am…
Comment: dittoHeatmap; adding column labels on the heatmap by jared.andrews07 ★ 18k
I'd consider making a [block annotation](https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#block-annotation…
Comment: Comparing GSEA mutant data to wild type by allingt • 0
What do you mean by "significant gene"? How did you perform GSEA and on how did you rank your genes for it? From guesswork I might initiall…
Comment: Genes of Interest in a Multi-Tissue Analysis by allingt • 0
The DESeq2 manual tells us that the object class of vst() output is a subclass of RangedSummarizedExperiment. I suspect the methods applica…
Comment: WGCNA: Why are my brown, yellow, and other modules not visible in the gene dendr by allingt • 0
Did you perform blockwise module detection by any chance? Are your results object's contents sorted in blocks?
Comment: Why does WGCNA use weighted correlation instead of Pearson correlation? by allingt • 0
The WGCNA implementation by Langfelder and Horvath provides various correlation methods to create the initial correlation matrix. I don't t…
Comment: dittoHeatmap; adding column labels on the heatmap by Varun Gupta ★ 1.3k
any idea, how can I display the labels Pre and POst on the top of the heatmap? I am looking at complexheatmap package as to how they displa…
Comment: How can I determine the p-value of genes within each identified module in WGCNA? by allingt • 0
What p-value do you mean? When and how did you calculate it?
Answer: What is a genomic range that would almost always get decent WGS coverage but is by i.sudbery 20k
What about some of the well known enhancer regions, the globin locus LCR? Likely to be highly sequenceable, and yet not on exome panels.
Answer: Using NumReads column of quants.genes.sf file to build DESeq2 input by i.sudbery 20k
One of the improvements that the using the `salmon` -> `tximport` -> `DESeq2` pipeline, over just a `counts`->`DESeq2` pipeline is the abil…
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