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Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing housekeeping Single-cell normalization
updated 12 minutes ago by 82k • written 46 minutes ago by • 0
0
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0
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33
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Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
3 hours ago by avocado123 • 0
0
votes
0
replies
30
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How to calculate correlation coefficient for chipseq?
chipseq bigwigsummary correlation
3 hours ago by Emily ▴ 10
0
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0
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37
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How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds kaks VCF
3 hours ago by rohitsatyam102 ▴ 840
0
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0
replies
34
views
how to read graph_test output of monocle 3
monocle3
4 hours ago by synat.keam ▴ 100
0
votes
1
reply
368
views
GAPIT p-value significance threshold
GAPIT p-value GWAS
updated 5 hours ago by • 0 • written 4 months ago by • 0
0
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0
replies
54
views
Why not use iBAQ for calculating differential abundance of proteins?
protein maxquant
11 hours ago by Aspire ▴ 300
0
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2
replies
132
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Highest variable features in single cell data
cell single
9 hours ago by Kazo • 0
0
votes
1
reply
120
views
PCA plot
DESeq2 PCAplot
updated 5 hours ago by ▴ 170 • written 16 hours ago by ▴ 10
0
votes
0
replies
81
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein pdb alpha-carbon
19 hours ago by 4fzcgueyp5 • 0
0
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1
reply
134
views
Annovar using R package
Annovar gnomAD R
updated 21 hours ago by 161k • written 1 day ago by ▴ 40
0
votes
5
replies
258
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 6 hours ago by 141k • written 1 day ago by ▴ 90
0
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0
replies
107
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA GDCprepare
updated 1 day ago by 43k • written 1 day ago by • 0
0
votes
0
replies
201
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome PGAP NCBI roary Prokka
1 day ago by pramach1 ▴ 40
0
votes
1
reply
125
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate GEMMA GWAS
updated 1 day ago by • 0 • written 1 day ago by • 0
0
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0
replies
110
views
Sequence BLAST in plus/minus and plus/plus
blast CRISPR strand sequencing
1 day ago by salias • 0
0
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4
replies
233
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
11 hours ago by sehriban.buyukkilic ▴ 10
0
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0
replies
98
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq single-cell suppa alternative-splicing
updated 1 day ago by 43k • written 1 day ago by • 0
1
vote
2
replies
178
views
alignment result
RNA-seq samtools hisat2
14 hours ago by ahmad.sajad4541 • 0
0
votes
0
replies
89
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet DoubletFinder Seurat modelHomotypic
updated 1 day ago by 43k • written 1 day ago by • 0
0
votes
0
replies
102
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile scvelo scipy annData numpy
1 day ago by Kash ▴ 110
0
votes
1
reply
138
views
How to solve this RoseTTAFold colaboratory error?
modeling Google Colaboratory RoseTTAFold protein
updated 1 day ago by ★ 27k • written 1 day ago by • 0
0
votes
2
replies
227
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein FASTA alignment
updated 1 day ago by 43k • written 1 day ago by ▴ 140
2
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9
replies
813
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 1 day ago by 4.2k • written 6 months ago by • 0
0
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10
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396
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How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
1 day ago by atowns21 • 0
0
votes
1
reply
145
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering subclustering scRNAseq
updated 2 days ago by ★ 2.3k • written 2 days ago by • 0
0
votes
0
replies
91
views
The concept of co-occurrence network structure
co-occurence microbiome network
2 days ago by ohtang7 ▴ 40
0
votes
1
reply
148
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs methylkit
updated 2 days ago by 141k • written 2 days ago by ▴ 20
0
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5
replies
280
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
1 day ago by njornet ▴ 20
0
votes
0
replies
84
views
Software to calculate RSCU, ENC other than codonw
rscu codonw
updated 2 days ago by 43k • written 2 days ago by • 0
0
votes
0
replies
93
views
Merging replicates from Encode project
CHIP-seq encode
2 days ago by Nurken • 0
1
vote
3
replies
198
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools bam splicing
2 days ago by WouterDeCoster 47k
1
vote
3
replies
236
views
some error in building kraken2 database
metagenome kraken2
1 day ago by Art1ess • 0
0
votes
1
reply
125
views
Subset Seurat object from Xenium spatial data
Seurat Xenium Spatial
updated 2 days ago by ★ 2.3k • written 2 days ago by ▴ 110
1
vote
1
reply
160
views
Failed kmer content
kmer illumina ngs
updated 2 days ago by 43k • written 2 days ago by • 0
0
votes
0
replies
81
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy Copy-number-analysis R
updated 2 days ago by 43k • written 2 days ago by • 0
0
votes
1
reply
140
views
Identification of Transgene insertion sites
Transgene Whole-Genome-Sequencing transgene-sites
updated 3 days ago by 43k • written 3 days ago by • 0
0
votes
8
replies
293
views
Error in cnetplot enrichplot package
R
updated 2 days ago by 43k • written 3 days ago by • 0
0
votes
0
replies
105
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment Genomics Ka-Ks
updated 3 days ago by 43k • written 3 days ago by ▴ 200
0
votes
0
replies
89
views
Analysis of the gene family of a genome.
Genome gene-family
updated 3 days ago by 43k • written 3 days ago by ▴ 80
0
votes
0
replies
92
views
File with NCBI summary or Uniprot description
annotation visualisation NCBI Uniprot RNA
updated 2 days ago by 43k • written 3 days ago by • 0
0
votes
0
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177
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS Meta-analysis
updated 3 days ago by 43k • written 3 days ago by ▴ 10
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink PED
updated 2 days ago by 10k • written 6.1 years ago by ▴ 10
1
vote
5
replies
253
views
Downsampling fastq file
downsample fastq
updated 3 days ago by 43k • written 3 days ago by ▴ 80
0
votes
1
reply
124
views
tbtool
tbtool
updated 3 days ago by 43k • written 3 days ago by • 0
0
votes
2
replies
188
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 3 days ago by 19k • written 3 days ago by • 0
0
votes
1
reply
119
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq nucleosome fragment
updated 3 days ago by 82k • written 3 days ago by • 0
0
votes
0
replies
82
views
Help with finding conferences in immuno-informatics/virology
virology conferences immunology
3 days ago by manaswwm ▴ 490
0
votes
0
replies
73
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
2 days ago by alifafiq1 • 0
0
votes
0
replies
80
views
How to get somatic variation based on RNA-seq data?
RNA-seq variation somatic
3 days ago by feather-W • 0
1,000 results • Page 1 of 20
Recent Votes
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
Comment: Why gatk VariantAnnotator required bam and coverage files
A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
Answer: How do I get the 3bp sequence on either side of a co-ordinate
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Scholar to ATpoint 82k
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Recent Replies
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 : 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 ▴ 840
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). | …
Answer: Sequence read length shorter than flow cell specification by ATpoint 82k
It is the amount of reagent in the kit that determines read length. Sometimes index cycle reagents are allocated to R1/R2 or they used anot…
Comment: Why gatk VariantAnnotator required bam and coverage files by Pierre Lindenbaum 161k
you don't need the bam file https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator : VariantAnnotator …
Comment: GAPIT p-value significance threshold by ginellegrenier • 0
Hi, I was wondering if you have found a solution to this? Thanks!
Comment: PCA plot by jkim ▴ 170
cross posted in bioconductor. [https://support.bioconductor.org/p/9157968/][1] [1]: https://support.bioconductor.org/p/9157968/
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