Limit : all time
all time today this week this month this year
121,965 results • Page 214 of 2440
Sort: Rank
Rank Views Votes Replies
1
vote
2
replies
2.7k
views
What is an appropriate cut off for p-values and log fold changes during the analysis of a time course global gene expression experiment using DESeq2?
LFC Deseq2 p-value
updated 2.1 years ago by ▴ 380 • written 2.1 years ago by ▴ 60
4
votes
1
reply
1.3k
views
Herald: The Biostar Herald for Monday, August 28, 2023
herald
updated 2.1 years ago by ▴ 880 • written 2.1 years ago by 3.6k
3
votes
7
replies
2.0k
views
GATK AnnotateVcfWithBamDepth returns zero DP for all variants in VCF
GATK AnnotateVcfWithBamDepth
2.1 years ago by ClkElf ▴ 50
4
votes
5
replies
2.1k
views
SRA and Bioproject IDs
Bioproject GEO SRA
updated 2.1 years ago by 154k • written 2.1 years ago by ▴ 80
1
vote
11
replies
2.3k
views
Quantification after transcriptome assembly with Trinity
De-novo-transcriptome-assembly Trinity RNA-seq-analysis
updated 2.0 years ago by 154k • written 2.1 years ago by ▴ 70
1
vote
2
replies
1.3k
views
Get the "average" of a column in a heatmap, combine 3 heatmaps into 1?
heatmap RNA-seq
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 40
0
votes
4
replies
2.1k
views
CDHIT para and cdhit slow speed
processing cdhit-para DNA cdhit
updated 2.1 years ago by • 0 • written 2.2 years ago by ▴ 10
0
votes
0
replies
1.4k
views
Job: Bioinformatician at Max Planck Institute for plant breeding research (Cologne, Germany)
bioinformatician
2.1 years ago by microfuge ★ 2.0k
1
vote
0
replies
517
views
ENA submission organelle trans_table conflict
submission ENA transl_table organelle
2.1 years ago by RvV ▴ 30
1
vote
3
replies
1.5k
views
microarray DEG analysis
microarray DGE
updated 2.1 years ago by 89k • written 2.1 years ago by ▴ 60
2
votes
2
replies
842
views
Association Study
gwas Plink
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 10
0
votes
7
replies
2.8k
views
Converting string to numerical in bcftools
bcftools
updated 2.1 years ago by • 0 • written 2.2 years ago by • 0
0
votes
0
replies
635
views
conform-gt error "Duplicate marker"
comfort-gt beagle
2.1 years ago by czqmeet • 0
0
votes
0
replies
546
views
Single cell multi-omics data integration in plants or animals
multiomics single-cell
2.1 years ago by KABILAN ▴ 130
5
votes
1
reply
1.2k
views
Single-end strand specific Rna-Seq: Which strand that the reads from.
mRNA Single-end strand-specific TruSeq
updated 2.1 years ago by ★ 2.0k • written 2.1 years ago by ★ 1.3k
0
votes
1
reply
1.1k
views
cuffmerge erorr "ValueError: can't have unbuffered text I/O"
cuffmerge
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
2
votes
4
replies
1.4k
views
how to filter a multi-sample VCF file based on 0/0 genotype numbers
genotype VCF CNV
2.1 years ago by reza ▴ 300
1
vote
1
reply
871
views
Quantifying genes' expression with Trinity
De-novo-transcriptome-assembly Trinity RNA-seq-analysis
updated 2.1 years ago by ★ 1.3k • written 2.1 years ago by ▴ 70
4
votes
3
replies
1.2k
views
Fetch genomic region(s) from refseq genomes
ensembl
updated 2.1 years ago by 154k • written 2.1 years ago by ▴ 10
0
votes
2
replies
1.2k
views
Change mounted drive on GCP Batch nextflow process
google-cloud-platform unix nextflow
2.1 years ago by dthorbur ★ 3.1k
3
votes
5
replies
1.6k
views
Creating a Trinity assembly
De-novo-transcriptome-assembly Trinity RNA-seq-analysis
updated 2.1 years ago by ★ 1.3k • written 2.1 years ago by ▴ 70
0
votes
0
replies
648
views
News: Course. -Multivariate Data Analysis with R and vegan
R vegan MultivariateDataAnalysis
2.1 years ago by Physalia-courses ★ 2.6k
1
vote
3
replies
1.3k
views
Filtering transcription factor and HOMER and ENCODE
ENCODE Transcription-factor HOMER
2.1 years ago by qudrat.nii ▴ 40
0
votes
1
reply
1.1k
views
Problems with bcf concat
bcftools VCF
updated 2.1 years ago by 166k • written 2.1 years ago by • 0
6
votes
8
replies
2.1k
views
Recapitulating a GenomeBrowser-style plot
IGV genome-browser
10 months ago by LChart 5.1k
2
votes
3
replies
1.9k
views
Can I using scVI to integrate data, then using R to conduct following analysis?
R python single-cell
2.1 years ago by Andy ▴ 120
2
votes
2
replies
1.1k
views
heatmap() in r assigning incorrect scale color to only first column values
r heatmap
2.1 years ago by Jen ▴ 100
1
vote
3
replies
1.3k
views
ABSOLUTE not anymore on the GenePattern
cancer copy-number ABSOLUTE
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
1
vote
1
reply
829
views
bcftools update ID keeping only string after ';'
bcftools
updated 2.1 years ago by 166k • written 2.1 years ago by ▴ 890
2
votes
3
replies
1.8k
views
LD score table for East Asians used for BOLT-LMM
BOLT-LMM SNP LDSC
updated 2.1 years ago by 5.1k • written 2.2 years ago by ▴ 190
1
vote
0
replies
583
views
Single cell Multi omics data integration in agricultural data
multiomics
updated 2.1 years ago by 154k • written 2.1 years ago by ▴ 10
0
votes
5
replies
1.3k
views
Single Cell Pipeline for SmartSeq
scRNA-seq SmartSeq single-cell
written 2.1 years ago by • 0
4
votes
7
replies
3.2k
views
Help with Error: None of the requested features were found: PECAM1 in slot data
seurat multiome
2.1 years ago by Chris ▴ 360
0
votes
0
replies
674
views
Help with analyze single cell multiome (RNA and ATAC-seq)
seurat signac multiome
2.1 years ago by Chris ▴ 360
3
votes
5
replies
1.7k
views
BedGraph to bigwig inside Pipe?
bigwig bedGraph pipe
updated 2.1 years ago by 5.1k • written 2.1 years ago by ▴ 40
0
votes
0
replies
489
views
Using the Same Background for ATAC-seq Peak Calling Across Two Samples
ATAC-seq peak-calling chromatin-accessibility
2.1 years ago by David • 0
0
votes
0
replies
912
views
reading files after defining a directory path in Shiny R
Rshiny shinyapp selectdirectory
2.1 years ago by SHN ▴ 40
1
vote
1
reply
1.4k
views
Do I need to perform basic filtering before using scrublet?
scanpy scrublet
updated 2.1 years ago by 154k • written 2.1 years ago by ▴ 160
2
votes
5
replies
3.7k
views
Uniprot Database for download
proteomics Uniprot
updated 2.0 years ago by ★ 2.4k • written 2.1 years ago by ▴ 40
1
vote
1
reply
779
views
Bioinformatics or computer science
career PhD
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
4
votes
2
replies
1.7k
views
News: NCBI BLAST+ 2.14.1 Now Available
NCBI BLAST
2.1 years ago by PeterC_NCBI ▴ 520
8
votes
9
replies
2.5k
views
PCA proteomic DEP
PCA DEP
updated 2.1 years ago by 89k • written 2.1 years ago by ▴ 370
1
vote
1
reply
923
views
Can I utilize visualization tools in PARTEK to create plots, graphs, and visual summaries RNA editing analysis results to interpret and communicate y…
Partek RNA-editing Visualization
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
0
votes
2
replies
1.2k
views
Accidental flip of "control" and "comparison" group for differential gene expression analysis
Spatial-Transcriptomics RNA-seq
2.1 years ago by ivingan • 0
2
votes
2
replies
1.0k
views
Error in make STAR
STAR
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
0
votes
0
replies
606
views
Failed installation of OpenMS
OpenMS mass-spectrometry
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
3
votes
4
replies
2.2k
views
Fasta file is not converting properly to Indexed Fasta File
Jbrowse2 Samtools Fasta
updated 2.1 years ago by 154k • written 3.1 years ago by ▴ 30
1
vote
1
reply
644
views
Data integration in scRNAseq
scRNA-seq
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
0
votes
0
replies
571
views
Any recommended tools to compare the gene-gene network
gene-gene-network
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 40
9
votes
6
replies
3.3k
views
Problems using ERCC spike-ins for normalization in DESeq2
Spike-ins Differential-expression DESeq2 RNA-seq
2.1 years ago by manuel.fernandez ▴ 50
121,965 results • Page 214 of 2440
Recent Votes
Answer: How to create a consensus of a contig with samtools or bbmap?
Comment: Getting just fastqc.zip file?
alternate allele frequency and minor allele frequency
Calculating minor allele frequency for GnomAD VCF file
Hiring FT Remote Nextflow engineer to build ML workflows for cancer genomics
Answer: Gene expression equivalent of polygenic risk score ?
A: TRF output to .gff file
Recent Locations • All
Hong Kong, 24 minutes ago
France/Nantes/Institut du Thorax - INSERM UMR1087, 34 minutes ago
USA, 35 minutes ago
Perth, Australia, 37 minutes ago
Oviedo, 3 hours ago
United Kingdom, 4 hours ago
United States, 4 hours ago
Recent Awards • All
Popular Question to itparanoia • 0
Popular Question to arshad1292 ▴ 110
Popular Question to marongiu.luigi ▴ 760
Popular Question to a615ebfb ▴ 60
Popular Question to predeus ★ 2.1k
Popular Question to raquel • 0
Popular Question to Jeremy Leipzig 23k
Recent Replies
Comment: How to create a consensus of a contig with samtools or bbmap? by marongiu.luigi ▴ 760
sorry, I have mistaken samtools with spades... running `samtools view -h...` did the trick. Thank you.
Comment: Help with Ideathon by V K • 0
Thank you for the response! Unfortunately this is completely independent and not part of a course. I was asking for some innovative ways to…
Answer: How to create a consensus of a contig with samtools or bbmap? by lieven.sterck 16k
You assembled a genome using samtools ???? that sounds very weird, if not impossible ... The header (SQ lines) is missing from your file b…
Answer: gnomad par region variants by benformatics 4.2k
The XX and XY counts are present on any given variants page.
Comment: Help with Ideathon by Mensur Dlakic ★ 30k
I don't see a single question here. Saying `I need your expert help in figuring out how I can make this analysis useful!` is too open-ended…
Comment: Differences between published differential gene expression results and own analy by ATpoint 89k
Please link the paper, lets see their methods. With human data it can well be that they included something like surrogate variables to damp…
Comment: Differences between published differential gene expression results and own analy by dsull ★ 7.7k
There are many ways to do normalization and one of the correct ways is simply to plug raw counts into deseq2 (the math that deseq2 uses to …
Comment: tximport error (medianLengthOverIsoform) by rfran010 ★ 1.6k
Is it the version number in your data? e.g. ENST00000415118.1 vs ENST00000415118 could be causing the mismatch?
Comment: Differences between published differential gene expression results and own analy by vernonlim98 • 0
So is there any correct way for normalisation? I know limma recommends CPM via limma-voom and DESeq2 just takes in raw counts and does thei…
Comment: Gene expression equivalent of polygenic risk score ? by Picasa ▴ 690
Thanks a lot for your answer. I will check the paper.
Comment: Differences between published differential gene expression results and own analy by dsull ★ 7.7k
If those logFCs are different, then that's a normalization issue. The logFC is straight forward arithmetic (it's simply dividing mean of […
Comment: Differences between published differential gene expression results and own analy by vernonlim98 • 0
Thanks both for your input. It got me to look at the published methodologies more closely, and you guys were right. One paper that I was re…
Comment: Differences between published differential gene expression results and own analy by vernonlim98 • 0
Yes it does not match at all, and those genes that are common in both analysis results have very different logFC and p values
Comment: Errors with RSEM/bowtie2 by Olivia • 0
I am not sure what you mean by this, but I believe that is what I did. With Trinity, I matched all the paired reads together, so they shoul…
Answer: Gene expression equivalent of polygenic risk score ? by GouthamAtla 12k
I don't think something exists out of the box. With variants, we have a 'weight' for each variant on disease risk (obtained through large s…
Traffic: 3363 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6