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Rare Disease Variant Pathway Analysis
Pathway analysis
updated 2 hours ago by 4.2k • written 2 hours ago by ▴ 10
3
votes
3
replies
121
views
Sequence read length shorter than flow cell specification
illumina NGS sequencing
updated 3 hours ago by 14k • written 9 hours ago by • 0
0
votes
0
replies
36
views
Designing single-stable RNA molecules
structure RNA
3 hours ago by Edna • 0
0
votes
0
replies
41
views
How to visualize/predict the final transcript from Delly output?
WGS DELLY
3 hours ago by simplitia ▴ 130
0
votes
1
reply
66
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing housekeeping Single-cell normalization
updated 4 hours ago by 82k • written 5 hours ago by • 0
0
votes
2
replies
121
views
BLAST using both nucleotides and taxonomic local databases
blast ncbi taxid taxonomy
updated 6 hours ago by 141k • written 13 hours ago by ▴ 150
0
votes
2
replies
162
views
why renaming Idents in Seurat object doesn't work?
Seurat RenameIdents R
updated 2 hours ago by 43k • written 15 hours ago by ★ 1.8k
1
vote
1
reply
105
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign cell-markers
updated 4 hours ago by 43k • written 11 hours ago by ▴ 10
1
vote
2
replies
128
views
ScRNA data question
scRNA Vlnplot Samples
updated 7 hours ago by ▴ 10 • written 11 hours ago by ▴ 10
0
votes
0
replies
51
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
7 hours ago by avocado123 • 0
0
votes
0
replies
45
views
News: Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis Statistics R
updated 4 hours ago by 43k • written 7 hours ago by ★ 2.5k
0
votes
0
replies
42
views
How to calculate correlation coefficient for chipseq?
chipseq bigwigsummary correlation
7 hours ago by Emily ▴ 10
1
vote
0
replies
58
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds kaks VCF
8 hours ago by rohitsatyam102 ▴ 850
0
votes
0
replies
46
views
how to read graph_test output of monocle 3
monocle3
8 hours ago by synat.keam ▴ 100
0
votes
0
replies
63
views
Job: CTO/founding engineer role at Voyant Bio
engineer
8 hours ago by Assaf • 0
0
votes
1
reply
378
views
GAPIT p-value significance threshold
GAPIT p-value GWAS
updated 9 hours ago by • 0 • written 4 months ago by • 0
3
votes
4
replies
193
views
Why gatk VariantAnnotator required bam and coverage files
gatk VariantAnnotator
5 hours ago by QX • 0
2
votes
1
reply
135
views
Finding orthologs between genome error
OMA OMAbrowser
updated 15 hours ago by ★ 1.1k • written 1 day ago by • 0
0
votes
0
replies
61
views
Why not use iBAQ for calculating differential abundance of proteins?
protein maxquant
15 hours ago by Aspire ▴ 300
2
votes
4
replies
208
views
Fetch table from clinvar database according to a list of rsid
python clinvar perl
updated 4 hours ago by 43k • written 19 hours ago by ▴ 20
2
votes
3
replies
171
views
Figures are disappeared from html report of SnpEff
HTML SnpEff
updated 13 hours ago by 161k • written 17 hours ago by ▴ 30
0
votes
1
reply
114
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment gaps
updated 17 hours ago by ▴ 170 • written 18 hours ago by • 0
0
votes
2
replies
142
views
Highest variable features in single cell data
single-cell
updated 4 hours ago by 43k • written 17 hours ago by • 0
0
votes
1
reply
143
views
Network Alignment
plugin Cytoscape CytoMCS
updated 20 hours ago by ▴ 280 • written 1 day ago by ▴ 40
2
votes
4
replies
2.3k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi metagenomics centrifuge gi_taxid_nucl.dmp taxonomy
updated 20 hours ago by • 0 • written 2.4 years ago by • 0
0
votes
1
reply
136
views
PCA plot
DESeq2 PCAplot
updated 10 hours ago by ▴ 170 • written 21 hours ago by ▴ 10
0
votes
1
reply
124
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 4 hours ago by 43k • written 21 hours ago by ★ 3.9k
0
votes
3
replies
274
views
Heatmap and rna-seq
RNA-Seq Heatmap
updated 4 hours ago by 43k • written 2 days ago by ▴ 10
0
votes
4
replies
2.6k
views
Lositan freezing when generating selection table
LOSITAN
updated 22 hours ago by • 0 • written 8.3 years ago by • 0
0
votes
2
replies
173
views
Annovar using R package
Annovar gnomAD R
4 hours ago by DKA ▴ 40
3
votes
8
replies
472
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 19 hours ago by 14k • written 1 day ago by ▴ 10
1
vote
8
replies
742
views
Adding CB tag to bam file
samtools bam
updated 16 hours ago by 161k • written 7 days ago by • 0
0
votes
5
replies
267
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 11 hours ago by 141k • written 1 day ago by ▴ 90
0
votes
0
replies
96
views
News: 8th Berlin Summer School in NGS Data Analysis - Apply Now
DNA-seq variant-calling RNA-seq illumina transcriptomics
updated 4 hours ago by 43k • written 1 day ago by 11k
4
votes
7
replies
396
views
To get p-values for the TPM
P-value TPM RSEM
updated 16 hours ago by ★ 5.8k • written 1 day ago by • 0
0
votes
4
replies
240
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
16 hours ago by sehriban.buyukkilic ▴ 10
1
vote
2
replies
189
views
alignment result
RNA-seq samtools hisat2
18 hours ago by ahmad.sajad4541 • 0
0
votes
11
replies
413
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
58 minutes ago by atowns21 • 0
8
votes
15
replies
666
views
How to convert plink files to Hapmap Format
GWAS Plink
38 minutes ago by Sofia • 0
76
votes
72
replies
19k
views
19 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
22 hours ago by Kevin Blighe 87k
4
votes
2
replies
332
views
Missing protein (VEGF-A) in String db
VGFA stringdb
updated 10 minutes ago by • 0 • written 11 weeks ago by ▴ 20
0
votes
2
replies
573
views
Why cd-hit-est not work when sequence identity threshold<0.95？
genome cluster sequence
updated 22 hours ago by • 0 • written 21 months ago by • 0
3
votes
3
replies
2.3k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 10 hours ago by • 0 • written 22 months ago by ▴ 180
2
votes
6
replies
3.6k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell RNAseq DE Analysis Treatment Control
updated 4 hours ago by 82k • written 3.9 years ago by ▴ 280
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq SNP
updated 8 hours ago by ▴ 850 • written 6.1 years ago by ▴ 10
45 results • Page 1 of 1
Recent Votes
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Answer: Missing protein (VEGF-A) in String db
Missing protein (VEGF-A) in String db
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Recent Replies
Comment: Missing protein (VEGF-A) in String db by shalespringer • 0
Thank you for replying here; this helped me figure out why MAPK10 was missing from my results. It was also marked as a pseudogene in the En…
Comment: How to convert plink files to Hapmap Format by Sofia • 0
These are the first lines of the output: (Please is it normal to have NA in the P value column ?) CHR …
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by atowns21 • 0
So I used the barcodes that I created (combos of positions 1-10 and 11-20) and I obtained similar alignment stats as the paper I pulled the…
Comment: How to convert plink files to Hapmap Format by Sofia • 0
Thank you so much, it actually worked!
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 `…
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