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503 results • Page 1 of 11
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13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch-effect
updated 1 day ago by 43k • written 6.8 years ago by ★ 1.3k
11
votes
22
replies
4.1k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 8 days ago by 43k • written 5.0 years ago by ▴ 260
8
votes
10
replies
645
views
bash script
whole-genome-sequencing
updated 2 days ago by 43k • written 10 days ago by ▴ 30
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma microarray DEA batch-effect
updated 19 hours ago by 43k • written 4.7 years ago by ▴ 60
5
votes
2
replies
1.7k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq batch batch-effect sequencing
updated 1 day ago by 43k • written 2.9 years ago by ▴ 60
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
updated 7 days ago by • 0 • written 3.8 years ago by ★ 1.8k
5
votes
8
replies
3.6k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression RNA-seq gene-ontology
updated 8 days ago by 43k • written 6.5 years ago by ★ 1.6k
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression RNA-Seq GTex DESeq2
updated 8 days ago by 43k • written 6.4 years ago by ▴ 10
5
votes
6
replies
379
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot RNAseq Rstudio
updated 15 days ago by 100k • written 16 days ago by • 0
4
votes
6
replies
822
views
bwa mem hangs after a few thousand reads
bwa alignment variant-calling bwa-mem
updated 15 days ago by 43k • written 4 months ago by ▴ 30
4
votes
4
replies
347
views
Average expression of a sample in single-cell data
single-cell rna-seq
15 days ago by newuser2024 • 0
4
votes
7
replies
2.3k
views
Batch effects vs biological variables
Batch-effect DESeq2 combat_seq
updated 9 days ago by 43k • written 3.7 years ago by ▴ 20
4
votes
9
replies
540
views
variant calling
variant-calling
updated 14 days ago by 43k • written 15 days ago by • 0
4
votes
7
replies
538
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse JBrowse2
updated 16 days ago by ★ 3.8k • written 19 days ago by ▴ 140
4
votes
7
replies
521
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 4 days ago by 43k • written 5 days ago by ▴ 20
4
votes
13
replies
747
views
RNAseq of primary tumor and metastases in two different organ
metastases RNA-seq DEG R
updated 1 day ago by ★ 1.7k • written 6 days ago by • 0
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling samtools VCF BCF
updated 22 days ago by 43k • written 5.5 years ago by ▴ 110
3
votes
3
replies
302
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio volcano-plot
18 days ago by Pumla • 0
3
votes
12
replies
473
views
struggle to get fasta files from ucsc goldenPath
ucsc getfasta fasta
16 days ago by Lila M ★ 1.2k
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq combat rna-seq sva batch-effect
updated 1 day ago by 43k • written 21 months ago by ▴ 20
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression Salmon
updated 8 days ago by 43k • written 5.5 years ago by ▴ 100
3
votes
4
replies
332
views
Single cell analysis with "meta".tsv.gz file
Single-cell
15 days ago by Estevão • 0
3
votes
1
reply
254
views
how to change the gene header names in a fasta file?
fasta bioawk awk seqkit
updated 6 days ago by 43k • written 6 days ago by • 0
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq batch-effect DESeq2
updated 19 hours ago by 43k • written 4.4 years ago by ▴ 10
3
votes
2
replies
230
views
Gene reads all zero for each sample
R salmon DE DESeq2
20 days ago by DYLAN NICO • 0
3
votes
5
replies
390
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
updated 15 days ago by 141k • written 15 days ago by ▴ 190
3
votes
2
replies
209
views
Trying to write bwa mem -> samtools view -> samtools sort loop
bwa samtools mapping genome
updated 13 days ago by 161k • written 13 days ago by • 0
3
votes
2
replies
294
views
Seeking Guidance on How to Annotate Unusual Cell Populations in Single-Cell Data
Transcriptomics Single-Cell
updated 12 days ago by 43k • written 6 weeks ago by ▴ 20
2
votes
3
replies
243
views
P-value Threshold Consideration in Multi-Sample RNA-Seq Experiment
statistics RNA-Seq p-value
updated 15 days ago by 43k • written 16 days ago by • 0
2
votes
3
replies
1.5k
views
Duplicate row name not allowed while reading the file in R
RNA-Seq deseq2 Differential-Gene-expression R
updated 8 days ago by 43k • written 4.8 years ago by • 0
2
votes
6
replies
506
views
Need help understanding core SNPs
SNPs snippy
24 days ago by ujichu • 0
2
votes
2
replies
264
views
DepMap: siRNA and CRSIPR discrepancy
DepMap
updated 6 days ago by 81k • written 6 days ago by ★ 9.4k
2
votes
3
replies
250
views
Reference mouse phased vcf
mm10 vcf phasing Beagle
24 days ago by machoo • 0
2
votes
4
replies
293
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP CPU transcriptomics
19 days ago by Mohamed Abderrahmane ▴ 10
2
votes
6
replies
372
views
create a gene count matrix csv file from seurat object
Seurat sparseMatrix
9 days ago by jkim ▴ 170
2
votes
1
reply
232
views
Disease Prevalence Database/Disease Incidence Database
prevalence
updated 27 days ago by 43k • written 28 days ago by ★ 9.4k
2
votes
1
reply
160
views
multiple reference sequences
freebayes
updated 16 days ago by 141k • written 16 days ago by ▴ 10
2
votes
3
replies
924
views
Possible approach to select normal tissue samples for cancer RNA-Seq data without reference data for downstream analyses
R RNA-Seq DE batch-effect GTEx
updated 2 days ago by 43k • written 4.1 years ago by ▴ 790
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 1 day ago by 43k • written 7.4 years ago by • 0
2
votes
2
replies
624
views
Batch correction for DE analysis
batch-correction mRNA RNA-seq DEGs MDSplot
updated 1 day ago by 43k • written 2.6 years ago by ▴ 10
2
votes
2
replies
216
views
How to establish haplotype-specific gene expression levels
RNA-seq Haplotype
7 days ago by javanokendo ▴ 60
2
votes
4
replies
369
views
Per Base Sequence Content - continuous raise of G%
fastqc
updated 7 days ago by 141k • written 8 days ago by • 0
2
votes
4
replies
266
views
Addmetadata to seurat obj
seurat
7 days ago by synat.keam ▴ 100
2
votes
2
replies
259
views
A pipeline for prediction and annotation of obelisks
rna-seq
updated 21 days ago by 161k • written 22 days ago by ▴ 110
2
votes
5
replies
657
views
samtools mpileup taking too long
Bam samtools sam alignment
updated 12 days ago by 43k • written 5 weeks ago by • 0
2
votes
0
replies
181
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
3 days ago by Alexander ▴ 220
2
votes
1
reply
947
views
How to evaluate the performance of an RNA-seq pipeline
Differential-gene-expression RNA-Seq R DESeq2
updated 8 days ago by 43k • written 4.0 years ago by ▴ 300
2
votes
2
replies
1.6k
views
read count for RNA sequencing via nanopore
long-reads RNA-seq gene-expression read-count
updated 12 days ago by 43k • written 2.9 years ago by • 0
2
votes
2
replies
321
views
Seeking help with Tcga Target Gtex Expected Count Data
R TCGA gTEX
25 days ago by bioinfo_enthusiast • 0
2
votes
5
replies
322
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats hg002 bed homopolymer-regions
1 day ago by Bikram Kumar • 0
503 results • Page 1 of 11
Recent Votes
Answer: differential gene expression analysis when not all samples have an untreated cou
Answer: differential gene expression analysis when not all samples have an untreated cou
Answer: Sheep reference genome remapping coordinates
Answer: Sheep reference genome remapping coordinates
DEG analysis of RNA-seq data across multiple tissues and two conditions
Answer: Assume "yes" as the answer to any prompts with bioconda
Answer: Assume "yes" as the answer to any prompts with bioconda
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Recent Replies
Comment: Sheep reference genome remapping coordinates by valentinatsar • 0
Thank you for your response As I can understand this tool takes sequence input files right? I have genome-wide genotypes instead of sequen…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa by me ▴ 750
Ok I made this into an answer. Could you please accept it as such.
Answer: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa by me ▴ 750
You can't. The data does not exist. UniProt only annotates where a lysine is know to be acetylated. There is no way that UniProt can know w…
Comment: How to compare the quality of assemblies by GenoMax 141k
Are there any short read datasets available in SRA? Can you try and see how many left over reads remain after you align to both of your ass…
Comment: Korean human genome reference file by GenoMax 141k
From NCBI: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_001712695.1/ Use the `Download` button or `curl/datasets`.
Comment: SLURM submission problem: Indexing the Reference Genome is not done in STAR by GenoMax 141k
> But it keeps giving error Please tell us what the error is.
Answer: 10x VDJ (TCR/BCR) BAM to fastq by GenoMax 141k
Looking at the information about the BAM file in the link included at the end of this sentence, it seems that the BAM file does not contain…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa by Jacky • 0
I got it, thank you for your response.
Answer: DEseq2 by ATpoint 81k
The DESeq2 input is a numeric count matrix (or data.frame) with rows being genes/observations and columns being samples/cells/specimen. Ple…
Comment: How to add motifs in cellranger-arc reference? by Ehsan • 0
Hi. Do you have any updates on what you ended up doing? I am encountering same issue, cannot really find a good TF motif database for zebra…
Comment: biomaRt error for different R version by manaswwm ▴ 490
Wonderful, and thanks for tagging Mike! For those who come back for this problem, the following seemed to work for me: Downgrading `dbply…
Answer: Assume "yes" as the answer to any prompts with bioconda by Juke34 8.5k
From my experience using `biocontainers` base container no need to set `yes` installation is done without any command prompt, otherwise as …
Comment: SLURM submission problem: Indexing the Reference Genome is not done in STAR by Dave Carlson ★ 1.7k
You're allocating 4 compute nodes (`#SBATCH -N 4`), but STAR can't actually make use of more than 1 compute node. You can increase the num…
Answer: Assume "yes" as the answer to any prompts with bioconda by Dave Carlson ★ 1.7k
```conda install -y bioconda::packageX conda-forge::packageY``` should do what you're looking for.
Comment: Supergnova stuck in tutorial by Murat • 0
Hi GenoMax, Thank you for your advice. I sent an email to them and have already opened an issue on Github. Let see if there is any other so…
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