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1,000 results • Page
1 of 20
Sort: Rank
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Views
Votes
Replies
0
votes
0
replies
2
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
just now by
NorbertK
• 0
0
votes
1
reply
14
views
Differential Expression Analysis using DESeq2 in R
Bioinformatics
analysis
R
deseq2
updated 5 minutes ago by
ATpoint
82k • written 27 minutes ago by
Erina
• 0
0
votes
0
replies
13
views
WGCNA Module-Trait Heatmap
module_trait_heatmap
wgcna
heatmap
26 minutes ago by
mja
• 0
0
votes
1
reply
34
views
Downloading older version of a tool
Alignment
tools
updated 1 hour ago by
GenoMax
142k • written 1 hour ago by
Ruqaiya
• 0
0
votes
0
replies
23
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
2 hours ago by
rustykb
▴ 20
3
votes
5
replies
95
views
Generating mpileup file using samtools
mpileup
samtools
updated 1 hour ago by
Joe
21k • written 4 hours ago by
Ruqaiya
• 0
0
votes
1
reply
68
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 50 minutes ago by
dthorbur
★ 1.9k • written 7 hours ago by
Vijith
▴ 30
0
votes
0
replies
61
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
8 hours ago by
Jeyong
• 0
0
votes
0
replies
58
views
Empty table plot using plotGseaTable()
FGSEA
16 hours ago by
Chris
▴ 260
3
votes
8
replies
6.5k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 18 hours ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
114
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
18 hours ago by
dtnondorf
• 0
0
votes
1
reply
139
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 10 hours ago by
Chris Dean
▴ 390 • written 19 hours ago by
sovrappensiero
▴ 90
2
votes
6
replies
257
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
12 hours ago by
Qroid
▴ 40
0
votes
1
reply
100
views
Provean help
variant
Provean
updated 18 hours ago by
Mensur Dlakic
★ 27k • written 21 hours ago by
Arun Sai Kumar
• 0
0
votes
0
replies
76
views
Use of annotation of integrated Seurat object in single sample
Seurat
1 day ago by
Bine
▴ 60
0
votes
1
reply
197
views
Subsetting and merging back Seurat Object brings different results
Seurat
1 day ago by
Bine
▴ 60
1
vote
1
reply
121
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 21 hours ago by
Ram
43k • written 1 day ago by
marco.barr
▴ 90
0
votes
0
replies
74
views
edgeR contrasts for analysis of reciprocal hybrid crosses - averaging, pooling, and comparing groups
edgeR
1 day ago by
Rhiannon
• 0
0
votes
0
replies
83
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
1 day ago by
Vijith
▴ 30
0
votes
0
replies
85
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
1 day ago by
James
▴ 10
0
votes
1
reply
572
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 1 day ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
1
vote
3
replies
198
views
Odd alignment question/finding
Alignment
updated 4 hours ago by
barslmn
★ 2.1k • written 1 day ago by
poordumbsillyidiot
• 0
0
votes
1
reply
189
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 1 day ago by
GenoMax
142k • written 1 day ago by
mgranada3
▴ 30
0
votes
0
replies
85
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
1 day ago by
meck
• 0
0
votes
0
replies
116
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 1 day ago by
Ram
43k • written 1 day ago by
Oscar
▴ 10
0
votes
1
reply
133
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 1 day ago by
Ram
43k • written 1 day ago by
ernestine.kubi
• 0
0
votes
0
replies
100
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
1 day ago by
VITALA
• 0
1
vote
2
replies
234
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
1 day ago by
rianna.collins
• 0
0
votes
1
reply
170
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 2 days ago by
i.sudbery
19k • written 2 days ago by
Edmond
• 0
0
votes
0
replies
135
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
2 days ago by
O.rka
▴ 710
0
votes
1
reply
514
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 2 days ago by
Ram
43k • written 2 days ago by
Dr Huma Naz
• 0
0
votes
5
replies
343
views
Telescope issue
Telescope
RNA-seq
updated 1 day ago by
GenoMax
142k • written 2 days ago by
eleven11
• 0
1
vote
1
reply
218
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 2 days ago by
Ram
43k • written 2 days ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
273
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
2 days ago by
Nafi
• 0
1
vote
3
replies
261
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 2 days ago by
GenoMax
142k • written 2 days ago by
jeffrey.maurer.informatics
• 0
0
votes
1
reply
169
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated 1 day ago by
Adam
▴ 30 • written 3 days ago by
Ahiad Chen Zion
• 0
0
votes
0
replies
122
views
barcode of TCR-sequencing
barcode
3 days ago by
yueli7
▴ 250
0
votes
0
replies
116
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 2 days ago by
Ram
43k • written 3 days ago by
Alexandros
• 0
0
votes
1
reply
159
views
unable to get feature count results
featureCounts
updated 2 days ago by
Ram
43k • written 3 days ago by
Ravita
• 0
0
votes
3
replies
263
views
KEGG Pathways
r
RNA-seq
updated 2 days ago by
Ram
43k • written 3 days ago by
Sudip
• 0
0
votes
0
replies
125
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
3 days ago by
Bine
▴ 60
0
votes
0
replies
123
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
3 days ago by
8armed
• 0
1
vote
2
replies
218
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 2 days ago by
Ram
43k • written 3 days ago by
Ravita
• 0
0
votes
0
replies
107
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
3 days ago by
Adyasha
• 0
0
votes
0
replies
111
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
3 days ago by
fanglujing
▴ 60
0
votes
0
replies
126
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
3 days ago by
Jacob
• 0
0
votes
1
reply
178
views
Differential Accessibility
DiffBind
updated 3 days ago by
Ram
43k • written 3 days ago by
Shloka
• 0
0
votes
3
replies
273
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 3 days ago by
GenoMax
142k • written 3 days ago by
kim
• 0
3
votes
7
replies
327
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
3 days ago by
salias
• 0
0
votes
0
replies
122
views
Using limma in methylation EM-seq?
EM-seq
methylation
3 days ago by
Lluís R.
★ 1.2k
1,000 results • Page
1 of 20
Recent Votes
Understanding ATAC-seq data
High Malat-1 expression in single cell data
Answer: DSEQ2 analysis
High Malat-1 expression in single cell data
Convert vcf files with phased genotypes to standard haplotype format
Convert vcf files with phased genotypes to standard haplotype format
A: Convert vcf files with phased genotypes to standard haplotype format
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e.r.zakiev
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dsull
★ 5.9k
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eebloom
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Recent Replies
Comment: Differential Expression Analysis using DESeq2 in R
by
ATpoint
82k
> everything is showing equal in environment section. But when I am checking for equalities, it’s showing False No idea what this means. P…
Answer: Analysis of intronic reads included scRNA-seq data
by
t.montserrat.ayuso
• 0
You can calculate the percentage of intronic reads for each cell using the [DropletQC][1] package for R. In this preprint we discuss th…
Comment: How does gene length effect the number of reads mapped
by
i.sudbery
19k
I did say almost - obviously things are going to get tricky at gene ends - this is why we have the concept of effective length. Its interst…
Answer: High Malat-1 expression in single cell data
by
t.montserrat.ayuso
• 0
Malat1 correlates with the intronic content and can be used as a nuclear indicator. In this preprint we discuss about this artifact and the…
Comment: How does gene length effect the number of reads mapped
by
dsull
★ 5.9k
I wouldn't say it's true that number of reads is linearly proportional to the length of the gene. That's just an assumption that people mak…
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
by
dthorbur
★ 1.9k
Using any of the species present would likely result in a resonable annotation set. You could use *Arabidopsis* since it likely has the mos…
Comment: Downloading older version of a tool
by
GenoMax
142k
Have you tried conda install <pkg>=<version> so conda install smalt=0.5.8 <!-- junk -->
Comment: Generating mpileup file using samtools
by
Joe
21k
Older versions of software are usually available via distribution tools or the websites. It may require a lot of digging, but its almost ce…
Comment: RNA-seq data for deep learning classification
by
Yuju
• 0
Thank you very much for sharing your advice. Yes, it definitely makes sense that with the use of deep learning, models would learn normalis…
Comment: Generating mpileup file using samtools
by
Ruqaiya
• 0
I didn't use the same tool as in the paper...
Comment: read length in structural variant calling
by
eebloom
▴ 80
Yes good idea. I guess the quality of the SV calls and as a proxy for quality the length and distribution of variants called might be infor…
Comment: Generating mpileup file using samtools
by
Ruqaiya
• 0
I just realised I didn't align my reads with the tools they used and used bowtie2 instead. I can't download the older version that is menti…
Comment: Downsampling long-read BAM files
by
eebloom
▴ 80
This is not what I needed for this particular use case, as capping the coverage would lose the information on regions of copy number amplif…
Comment: Do I need to go back and filter my long-reads?
by
eebloom
▴ 80
Apologies, I deleted the question as I wasn't sure it would be helpful to others and it didn't seem to have a clear answer, not to snub the…
Comment: Do I need to go back and filter my long-reads?
by
eebloom
▴ 80
Thanks, I think it would be a good idea to track the results downstream to look for batch effects. I think I will filter the reads ultimate…
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