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Showing top results for tag: DE • reset
0
votes
2
replies
346
views
Find DE in single cell RNA sequencing
DE DESeq2 scRNAseq analysis
24 days ago by kayah ▴ 20
0
votes
0
replies
245
views
Passing list of genes to celltypist
DE SingleCell CellAnnotation CellTypist Python
12 weeks ago by Bioinformatics_begginner ▴ 20
0
votes
0
replies
168
views
Seurat-DE analysis
seurat DE
5 months ago by odi ▴ 10
3
votes
2
replies
377
views
Gene reads all zero for each sample
R salmon DE DESeq2
6 months ago by DYLAN NICO • 0
0
votes
2
replies
920
views
Downsampling of cells in scRNAseq DE analysis
differential-expression DE scRNAseq
updated 5 months ago by 44k • written 17 months ago by • 0
2
votes
6
replies
870
views
Differential expression analysis with very high duplication rate
RNA-seq DE Picard PCR duplicates
7 months ago by JMB ▴ 20
1
vote
9
replies
880
views
Approach for multi species comparative transcriptomics and differential expression analyses
DE RNA-seq transcriptomics
updated 8 months ago by ★ 2.4k • written 8 months ago by • 0
0
votes
0
replies
291
views
not best k value found
de assemblly assembly novo kmergenie
10 months ago by shaileshdesai76 • 0
2
votes
2
replies
513
views
how do I assemble centromere regions in a plant genome?
novo de assembly
updated 10 months ago by 47k • written 10 months ago by • 0
0
votes
0
replies
362
views
DE analysis in paired samples with limma
R DE limma
11 months ago by dv_f • 0
0
votes
5
replies
1.2k
views
Convert gene id's to gene symbol preserving gene id's in deseq2
ensembl r DE deseq2
updated 12 months ago by 44k • written 12 months ago by • 0
2
votes
4
replies
729
views
What to do after importing quantification with tximport
R transcriptome DE DESeq2
13 months ago by dylannicoembros • 0
4
votes
3
replies
1.1k
views
transcripts missing from tx2gene
R transcriptome DE DESeq2
14 months ago by dylannicoembros • 0
7
votes
6
replies
1.6k
views
On "wings" in volcano plots...
DEG volcano DGE statistics DE
updated 16 months ago by 84k • written 16 months ago by ▴ 270
0
votes
0
replies
366
views
pseudo-bulk
scRNAseq DE
updated 16 months ago by 44k • written 17 months ago by ▴ 10
0
votes
1
reply
506
views
Why do I get zero results when doing DE on microarray data with lemma?
microarray DE limma affymetrix
updated 17 months ago by ★ 2.0k • written 17 months ago by • 0
2
votes
2
replies
815
views
remove rRNA reads before DE analysis?
DE analysis
18 months ago by anubhav9 • 0
0
votes
0
replies
394
views
issue changing k values on SOAPdenovo2
novo de assembly
18 months ago by parrasevilla.bioinfo • 0
0
votes
0
replies
364
views
Metatranscriptomics: de novo assembly of mRNA per OTU?
MAGs no total novo metatranscriptomics assembly de MEGAN rna
18 months ago by Maria • 0
0
votes
4
replies
2.0k
views
WGCNA hub genes VS. DEG
DE analysis WGCNA DEG
18 months ago by Penny • 0
1
vote
2
replies
775
views
DeSeq2 Matched Analysis
rnaseq DE Deseq2
22 months ago by Andrea ▴ 10
3
votes
6
replies
1.7k
views
Multi factor analysis in DESeq2 and design formula
rnaseq DE statistics deseq design
23 months ago by nik.kraemer • 0
4
votes
2
replies
648
views
Manually adding genes of interest to transcriptome for RNASeq DE?
rnaseq de
updated 2.0 years ago by 4.0k • written 2.0 years ago by ▴ 20
6
votes
4
replies
5.7k
views
miRDeep2 output scores
miRDeep2 NGS miRNAs DE rna-seq
updated 2.0 years ago by • 0 • written 8.0 years ago by ▴ 180
2
votes
4
replies
987
views
DE analysis with multiple factors
DE DEP limma
2.0 years ago by Abhishek • 0
1
vote
1
reply
780
views
Merge Trinity assembly
de assembly novo kmer trinity
updated 2.1 years ago by ★ 1.3k • written 2.1 years ago by • 0
0
votes
0
replies
397
views
Comparing the regulators and Pathways induced by Differential Expression Analysis of two treatments at the same time point
timepoints Comparison RNA-Seq DE treatments
2.1 years ago by mkh ▴ 60
4
votes
2
replies
875
views
Feature selection for a binary classifier using mixed cancer type samples
genes training-test mixed samples split feature DE selection classifier
2.2 years ago by mmitra ▴ 60
0
votes
0
replies
335
views
Single cell
DE SC
2.2 years ago by shiviagarwalpharma • 0
2
votes
1
reply
510
views
How to do differential expressions in R from scRNAseq count files after scaling and normalization?
R scRNAseq DE
updated 2.3 years ago by ★ 17k • written 2.3 years ago by ▴ 10
7
votes
11
replies
2.5k
views
[R] How to make Contrast for Differential Expressed with more classes than 2 ?
de gene dge R edgeR
2.3 years ago by ali ▴ 20
0
votes
0
replies
338
views
Palimpsest deconvolution_fit() problem
palimpsest de mutation signature extraction novo
2.4 years ago by 15927207765 • 0
0
votes
4
replies
2.9k
views
Estimate K-mer size for de novo assembly
de novo assembly soapdenovo estimation kmergenie K-mer
updated 2.4 years ago by ★ 28k • written 2.4 years ago by ▴ 70
3
votes
7
replies
1.1k
views
How to analyze the differential expression of a gene if it has several ensembl id
data RNA-seq DE analysis
updated 2.4 years ago by 145k • written 2.4 years ago by • 0
1
vote
2
replies
614
views
microRNA PCR analysis
PCR expression DE microRNA differential
updated 2.5 years ago by 21k • written 2.5 years ago by • 0
4
votes
5
replies
2.1k
views
Volcano plot with aggregated p values from Sleuth
de kallisto log2fc rna-seq sleuth
updated 2.4 years ago by ★ 6.8k • written 2.5 years ago by • 0
0
votes
0
replies
305
views
Detecting de novo versus inherited variants using whole genome sequencing from duo
sequencing de genetics NGS genome novo
2.5 years ago by Anne • 0
2
votes
4
replies
1.6k
views
BAM > featurecount > DEseq2 Nextflow/Snakemake pipeline
DEseq2 DE RNA-Seq
2.5 years ago by MJ500 • 0
4
votes
3
replies
1.4k
views
lncRNA quantification featurecounts
featurecounts TCGA lncRNA DE
updated 2.6 years ago by 3.2k • written 3.0 years ago by ▴ 10
2
votes
2
replies
643
views
Low number of differentially expressed genes in scRNAseq
DEgenes scRNAseq DE analysis
updated 2.6 years ago by 84k • written 2.6 years ago by • 0
3
votes
7
replies
2.2k
views
6 follow
What does an amino acid sequence that does not start with methionine mean?
de Trinity novo assembly protein TransDecoder
updated 4 months ago by ★ 28k • written 2.6 years ago by ▴ 80
0
votes
0
replies
458
views
Estimating power in RNA-seq differential expression
RNA-seq edgeR Expression DE Differential
2.7 years ago by ams686 • 0
0
votes
1
reply
668
views
transcript id for gene id in ballgown
R DE ballgown
updated 13 months ago by 44k • written 2.7 years ago by • 0
0
votes
0
replies
523
views
Prioritizing/rank ordering genes from two lists: averaging values?
gene RNA-seq DE list ranking
2.3 years ago by kelen ▴ 210
3
votes
6
replies
2.0k
views
How to collapse de novo contigs into a single sequence?
genome de contigs assembly spades bruijn
2.8 years ago by marongiu.luigi ▴ 710
1
vote
2
replies
4.3k
views
Read Counts from miRDeep2 for posterior DE analysis
mirdeep2 RNA-Seq DE read counts miRNAs
updated 2.9 years ago by ▴ 130 • written 8.0 years ago by ▴ 180
0
votes
3
replies
1.1k
views
How much differential RNA expression is expected between male and female in a random tissue?
DE RNA limma
updated 2.9 years ago by ▴ 500 • written 2.9 years ago by ▴ 10
3
votes
2
replies
952
views
Should limma DE results from FPKM data make at least certain sense?
DE FPKM limma
2.9 years ago by nvera ▴ 10
0
votes
0
replies
452
views
For DE analysis, should I exclude all the samples that don't have the data of normal tissue?
TCGA RNA-seq DE
3.0 years ago by Sonia • 0
1
vote
11
replies
2.6k
views
How to perform DE anaysis on a data set in which biological replicates have high varaince?
high replicates biological variance DE
3.0 years ago by Gisele • 0
50 results • Page 1 of 1
Recent Votes
Answer: Importing data from GEO
Importing data from GEO
A: 0 Features for COVID-19 ExpressionSet through GEOQuery
0 Features for COVID-19 ExpressionSet through GEOQuery
Comment: trying to use the API for edirect tool (NCBI)
Using GEOquery
Answer: The Evolution of NGS: What’s New and What’s Next?
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Recent Replies
Comment: Using GEOquery by Rohulla • 0
I also come up with this problem. No body still answer this question.
Answer: Performing Needleman-Wunsch Global Alignment for multiple mutant proteins agains by Istvan Albert 101k
You can use the `bio` with the `align` tool. Install with `pip install bio` then bio align query.fa target.fa You can put all the tar…
Answer: Long-read sequencing data simulation using CAMISIM by Istvan Albert 101k
Since they explicitly have a pbsim config file, the comment you found is probably just a leftover from another config file that was copied …
Comment: RNA-Seq mutation calling without germline data by marionette.kent • 0
Thanks @shred for sharing your pipeline. Can I ask if it runs each sample individually? Our HPC has limited space for each user so I have b…
Comment: Pedigree information by bk11 ★ 3.0k
Since you have plink (bed/bim/fam) files, sex information is stored in the 5th column of the `.fam` file. If that information is missing an…
Comment: The Evolution of NGS: What’s New and What’s Next? by i.sudbery 20k
I know its a technical possiblity. But people I know that do this say its still very much an experimental technique. You need to learn the …
Answer: Merging bfiles by bk11 ★ 3.0k
If you have common set of SNPs between your two set of bfiles `(PLINK files)`, you can use `plink --bmerge` command to merge them as follow…
Comment: The Evolution of NGS: What’s New and What’s Next? by Istvan Albert 101k
`rust` was not designed to be a competitor to `python`, it was designed as a competitor to `C` and `C++` - `rust` integrates really well…
Comment: Can someone install me (remotely) Amber24? by Ram 44k
Do you mean you have a Windows machine that has Windows Subsystem for Linux and you're unable to install a piece of software over a remote …
Comment: Choosing the Best Method for DEG Analysis: limma vs. DESeq2 for RSEM Normalized by Istvan Albert 101k
Fundamentally these types of filterings come down to the effect they have on the data. Does your filtering change the data, does it chang…
Comment: Generally how are non-canonical chromosomes treated in human variation studies by GenoMax 145k
This blog post may partly help: https://lh3.github.io/2017/11/13/which-human-reference-genome-to-use
Comment: Why does assigning genes with biomart give me different values than using a tran by bioinfo ▴ 150
Do you think that I should be including the information from the scaffold patch for the quantification? Initially I used the transcript_to_…
Comment: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an by GenoMax 145k
It has been moved to a comment (looks like you are a moderator that seems to have come back after a long break). You can accept @dgtool ans…
Answer: Mendelian precison by Pierre Lindenbaum 164k
For trios and short-reads, I use delly or manta to get a join VCF of the trio (+ a few controls to discard false positives). I then kee…
Comment: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an by Ian 6.1k
Thank you your suggestion on using -O worked. Makes sense in hind-sight. Sorry I couldn't select your answer as the "winner" as you poste…
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