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522 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 8 days ago by 43k • written 6.8 years ago by ★ 1.3k
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 16 days ago by 43k • written 5.0 years ago by ▴ 260
8
votes
10
replies
697
views
bash script
whole-genome-sequencing
updated 10 days ago by 43k • written 17 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 8 days ago by 43k • written 4.7 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 15 days ago by • 0 • written 3.8 years ago by ★ 1.8k
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression RNA-Seq GTex DESeq2
updated 16 days ago by 43k • written 6.4 years ago by ▴ 10
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression RNA-seq gene-ontology
updated 16 days ago by 43k • written 6.5 years ago by ★ 1.6k
5
votes
6
replies
393
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot RNAseq Rstudio
updated 23 days ago by 100k • written 24 days ago by • 0
5
votes
2
replies
1.7k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq batch batch-effect sequencing
updated 9 days ago by 43k • written 2.9 years ago by ▴ 60
4
votes
6
replies
832
views
bwa mem hangs after a few thousand reads
bwa alignment variant-calling bwa-mem
updated 23 days ago by 43k • written 4 months ago by ▴ 30
4
votes
4
replies
359
views
Average expression of a sample in single-cell data
single-cell rna-seq
23 days ago by newuser2024 • 0
4
votes
7
replies
544
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 12 days ago by 43k • written 13 days ago by ▴ 20
4
votes
2
replies
226
views
Trying to write bwa mem -> samtools view -> samtools sort loop
bwa samtools mapping genome
updated 21 days ago by 161k • written 21 days ago by • 0
4
votes
13
replies
864
views
RNAseq of primary tumor and metastases in two different organ
metastases RNA-seq DEG R
updated 8 days ago by ★ 1.7k • written 14 days ago by • 0
4
votes
9
replies
568
views
variant calling
variant-calling
updated 22 days ago by 43k • written 23 days ago by • 0
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect DESeq2 combat_seq
updated 17 days ago by 43k • written 3.7 years ago by ▴ 20
4
votes
7
replies
559
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse JBrowse2
updated 23 days ago by ★ 3.8k • written 27 days ago by ▴ 140
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq combat rna-seq sva batch-effect
updated 9 days ago by 43k • written 21 months ago by ▴ 20
3
votes
1
reply
264
views
how to change the gene header names in a fasta file?
fasta bioawk awk seqkit
updated 13 days ago by 43k • written 14 days ago by • 0
3
votes
5
replies
408
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
updated 22 days ago by 141k • written 23 days ago by ▴ 200
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression Salmon
updated 16 days ago by 43k • written 5.5 years ago by ▴ 100
3
votes
2
replies
300
views
Seeking Guidance on How to Annotate Unusual Cell Populations in Single-Cell Data
Transcriptomics Single-Cell
updated 20 days ago by 43k • written 7 weeks ago by ▴ 20
3
votes
4
replies
3.4k
views
any recommended tools for batch effect and normalization not written in R?
R RNA-Seq combat python batch-effect
updated 7 days ago by 43k • written 7.1 years ago by ▴ 310
3
votes
12
replies
491
views
struggle to get fasta files from ucsc goldenPath
ucsc getfasta fasta
23 days ago by Lila M ★ 1.2k
3
votes
3
replies
466
views
Free/open source 23andme-like analysis
SNPs genomics NGS VCF
updated 5 days ago by 14k • written 6 days ago by ▴ 510
3
votes
3
replies
316
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio volcano-plot
26 days ago by Pumla • 0
3
votes
2
replies
239
views
Gene reads all zero for each sample
R salmon DE DESeq2
28 days ago by DYLAN NICO • 0
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq batch-effect DESeq2
updated 8 days ago by 43k • written 4.4 years ago by ▴ 10
3
votes
4
replies
353
views
Single cell analysis with "meta".tsv.gz file
Single-cell
23 days ago by Estevão • 0
2
votes
3
replies
254
views
P-value Threshold Consideration in Multi-Sample RNA-Seq Experiment
statistics RNA-Seq p-value
updated 23 days ago by 43k • written 23 days ago by • 0
2
votes
1
reply
280
views
Forgot the web site with comparison of NGS platforms
NGS platforms
updated 26 days ago by ★ 3.8k • written 26 days ago by ▴ 110
2
votes
5
replies
669
views
samtools mpileup taking too long
Bam samtools sam alignment
updated 20 days ago by 43k • written 6 weeks ago by • 0
2
votes
4
replies
394
views
Per Base Sequence Content - continuous raise of G%
fastqc
updated 15 days ago by 141k • written 16 days ago by • 0
2
votes
1
reply
953
views
How to evaluate the performance of an RNA-seq pipeline
Differential-gene-expression RNA-Seq R DESeq2
updated 16 days ago by 43k • written 4.0 years ago by ▴ 300
2
votes
2
replies
264
views
singlecell annotation
scRNA-seq annotation
29 days ago by kayah • 0
2
votes
1
reply
165
views
multiple reference sequences
freebayes
updated 23 days ago by 141k • written 23 days ago by ▴ 10
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 8 days ago by 43k • written 7.4 years ago by • 0
2
votes
4
replies
292
views
Addmetadata to seurat obj
seurat
15 days ago by synat.keam ▴ 100
2
votes
2
replies
1.6k
views
read count for RNA sequencing via nanopore
long-reads RNA-seq gene-expression read-count
updated 20 days ago by 43k • written 2.9 years ago by • 0
2
votes
4
replies
2.6k
views
DESeq2 inconsistent results
differential-gene-expression RNA-Seq DESeq2
updated 16 days ago by 43k • written 8.1 years ago by ▴ 80
2
votes
2
replies
630
views
Batch correction for DE analysis
batch-correction mRNA RNA-seq DEGs MDSplot
updated 8 days ago by 43k • written 2.6 years ago by ▴ 10
2
votes
1
reply
245
views
VEP annotation --per_gene allele choice
VEP
updated 13 days ago by 43k • written 13 days ago by ▴ 10
2
votes
3
replies
928
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 10 days ago by 43k • written 4.1 years ago by ▴ 790
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 16 days ago by 43k • written 4.9 years ago by • 0
2
votes
18
replies
1.6k
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome phg_v2 plants PHG
23 days ago by b.contreras.moreira ▴ 170
2
votes
9
replies
815
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 1 day ago by 4.2k • written 6 months ago by • 0
2
votes
0
replies
1.8k
views
ComBat-seq adjustment of batch effects
RNA-Seq ComBat-seq SVA edgeR batch-effect
updated 8 days ago by 43k • written 3.4 years ago by ▴ 50
2
votes
0
replies
203
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
10 days ago by Alexander ▴ 220
2
votes
4
replies
301
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP CPU transcriptomics
27 days ago by Mohamed Abderrahmane ▴ 20
2
votes
6
replies
399
views
create a gene count matrix csv file from seurat object
Seurat sparseMatrix
17 days ago by jkim ▴ 170
522 results • Page 1 of 11
Recent Votes
Answer: Missing protein (VEGF-A) in String db
Missing protein (VEGF-A) in String db
Comment: Sequence read length shorter than flow cell specification
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
Detecting somatic variants in non-tumor tissue without normals
Answer: Sequence read length shorter than flow cell specification
Answer: Sequence read length shorter than flow cell specification
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Recent Replies
Answer: Rare Disease Variant Pathway Analysis by LauferVA 4.2k
Hi @efc1e545 , First a caveat. the information we most need in order to help guide you to a successful conclusion is not provided in thi…
Answer: Sequence read length shorter than flow cell specification by swbarnes2 14k
The company probably had you share your run with someone who needed the extra bases. So you get the extra bases free. Just use them unle…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by Ram 43k
Thank you, the `csvtk spread` is super useful. I usually import into R using `lapply` then `Reduce` using `merge` but this might be easier.
Comment: Annovar using R package by DKA ▴ 40
Thank you for your guidance. The thing is that I am unfamiliar with using such environments, unfortunately.
Comment: Treatment VS Control in Single Cell RNAseq analysis by ATpoint 82k
Open a new question, with details.
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets by ATpoint 82k
I recommend https://bioconductor.org/books/3.18/OSCA.basic/normalization.html as well as the "advanced" section in this book.
Comment: Why gatk VariantAnnotator required bam and coverage files by QX • 0
thank you!
Comment: Treatment VS Control in Single Cell RNAseq analysis by kilcdincer ▴ 10
Hello, I have more or less same experimental setting and was wondering how you proceeded with your analysis? Can I reach its GitHub reposit…
Comment: BLAST using both nucleotides and taxonomic local databases by GenoMax 141k
> I ask this as some BLAST command fields as scinames or sblastnames do not give any output with a classic nt BLAST If that information is…
Answer: BLAST using both nucleotides and taxonomic local databases by 5heikki 11k
This has been discussed [many times][1] [1]: https://www.biostars.org/p/76551/
Answer: why renaming Idents in Seurat object doesn't work? by Bioinfotec ▴ 10
I think when you give indent to seuObj : ```r Idents(seuObj) <- 'RNA_snn_res.0.1' ``` You may wrongly assign other value to it such as `…
Answer: ScRNAseq-How to correctly choose cell type marker genes by Bioinfotec ▴ 10
In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. F…
Answer: ScRNA data question by Bioinfotec ▴ 10
In violin plot, a dot represents a cell. Actually, the straight lines you see in your infected image just means these cells have the same e…
Comment: Sequence read length shorter than flow cell specification by GenoMax 141k
> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended If they sent data that is not what you…
Comment: How to know synonymous and non-synonymous SNPs from transcriptome sequencing by rohitsatyam102 ▴ 850
I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K). | …
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