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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
319
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
4 days ago by
NorbertK
• 0
0
votes
2
replies
246
views
Downloading older version of a tool
Alignment
tools
4 days ago by
Ruqaiya
• 0
0
votes
0
replies
146
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
4 days ago by
rustykb
▴ 20
3
votes
5
replies
279
views
Generating mpileup file using samtools
mpileup
samtools
updated 4 days ago by
Joe
21k • written 4 days ago by
Ruqaiya
• 0
2
votes
3
replies
283
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 4 days ago by
dthorbur
★ 1.9k • written 5 days ago by
Vijith
▴ 30
0
votes
0
replies
145
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
5 days ago by
Jeyong
• 0
0
votes
0
replies
134
views
Empty table plot using plotGseaTable()
FGSEA
4 days ago by
Chris
▴ 280
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 5 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
197
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
5 days ago by
dtnondorf
• 0
1
vote
7
replies
493
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
▴ 400 • written 5 days ago by
sovrappensiero
▴ 90
3
votes
8
replies
506
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
1 day ago by
Qroid
▴ 40
0
votes
1
reply
151
views
Provean help
variant
Provean
updated 5 days ago by
Mensur Dlakic
★ 27k • written 5 days ago by
Arun Sai Kumar
• 0
0
votes
0
replies
101
views
Use of annotation of integrated Seurat object in single sample
Seurat
5 days ago by
Bine
▴ 60
0
votes
1
reply
229
views
Subsetting and merging back Seurat Object brings different results
Seurat
5 days ago by
Bine
▴ 60
1
vote
1
reply
143
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 5 days ago by
Ram
43k • written 5 days ago by
marco.barr
▴ 90
0
votes
0
replies
97
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
6 days ago by
Vijith
▴ 30
0
votes
0
replies
99
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
6 days ago by
James
▴ 10
0
votes
1
reply
588
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 6 days ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
1
vote
3
replies
241
views
Odd alignment question/finding
Alignment
updated 4 days ago by
barslmn
★ 2.1k • written 6 days ago by
poordumbsillyidiot
• 0
0
votes
1
reply
208
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 6 days ago by
GenoMax
142k • written 6 days ago by
mgranada3
▴ 30
0
votes
0
replies
100
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
6 days ago by
meck
• 0
0
votes
0
replies
124
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 6 days ago by
Ram
43k • written 6 days ago by
Oscar
▴ 10
0
votes
1
reply
153
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 6 days ago by
Ram
43k • written 6 days ago by
ernestine.kubi
• 0
0
votes
0
replies
107
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
6 days ago by
VITALA
• 0
1
vote
2
replies
255
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
6 days ago by
rianna.collins
• 0
0
votes
1
reply
189
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 6 days ago by
i.sudbery
19k • written 7 days ago by
Edmond
• 0
0
votes
0
replies
147
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
7 days ago by
O.rka
▴ 710
0
votes
1
reply
684
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 7 days ago by
Ram
43k • written 7 days ago by
Dr Huma Naz
• 0
0
votes
5
replies
379
views
Telescope issue
Telescope
RNA-seq
updated 6 days ago by
GenoMax
142k • written 7 days ago by
eleven11
• 0
1
vote
1
reply
236
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 7 days ago by
Ram
43k • written 7 days ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
296
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
6 days ago by
Nafi
• 0
1
vote
3
replies
286
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 7 days ago by
GenoMax
142k • written 7 days ago by
jeffrey.maurer.informatics
• 0
0
votes
2
replies
228
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
18 hours ago by
Ahiad Chen Zion
• 0
0
votes
0
replies
128
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 7 days ago by
Ram
43k • written 7 days ago by
Alexandros
• 0
0
votes
1
reply
175
views
unable to get feature count results
featureCounts
updated 7 days ago by
Ram
43k • written 7 days ago by
Ravita
• 0
0
votes
3
replies
291
views
KEGG Pathways
r
RNA-seq
updated 7 days ago by
Ram
43k • written 7 days ago by
Sudip
• 0
0
votes
0
replies
135
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
7 days ago by
Bine
▴ 60
1
vote
2
replies
229
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 7 days ago by
Ram
43k • written 8 days ago by
Ravita
• 0
3
votes
3
replies
223
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
1 day ago by
Adyasha
• 0
0
votes
0
replies
116
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
8 days ago by
fanglujing
▴ 60
0
votes
0
replies
134
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
8 days ago by
Jacob
• 0
0
votes
1
reply
185
views
Differential Accessibility
DiffBind
updated 8 days ago by
Ram
43k • written 8 days ago by
Shloka
• 0
0
votes
3
replies
296
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 7 days ago by
GenoMax
142k • written 8 days ago by
kim
• 0
3
votes
7
replies
351
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
8 days ago by
salias
• 0
0
votes
0
replies
128
views
Using limma in methylation EM-seq?
EM-seq
methylation
8 days ago by
Lluís R.
★ 1.2k
0
votes
0
replies
125
views
Synteny analysis
bacterial
synteny
genome
updated 8 days ago by
GenoMax
142k • written 8 days ago by
Namil
• 0
0
votes
4
replies
267
views
Genbank File Format
gbkformat
7 days ago by
alenew.am
• 0
0
votes
0
replies
242
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
8 days ago by
SSSJec
• 0
0
votes
3
replies
222
views
Software to separate reads from different individuals
software
development
nanopore
updated 8 days ago by
GenoMax
142k • written 8 days ago by
njornet
▴ 20
0
votes
2
replies
257
views
How to update R on ubuntu
installation
update
R
apt-get
8 days ago by
Bosberg
▴ 50
1,000 results • Page
2 of 20
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removeBatchEffect explained using base R linear models
Answer: ChIP-seq datasets: input samples omitted?
Answer: ChIP-seq datasets: input samples omitted?
Answer: Is therer any suggestions on mapping rate of WGBS data?
A: Download full list of SNPs and their coordinates in hg38
Answer: HCL database download
Answer: Tissue-specific DEG analysis with DEseq2
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Recent Replies
Answer: CNVKIT - unable to produce scatter and diagram pdfs
by
Anitha
• 0
Hello everyone, I need to call the CNV from my WGS data. I searched for many tutorial, but I did'nt get any proper procedure. I am trying t…
Comment: High Malat-1 expression in single cell data
by
t.montserrat.ayuso
▴ 30
I don't think dropout is playing an important role with Malat1 since it is usually highly expressed. On the other hand, if dropout is still…
Comment: java out of memory error through beagle for imutation
by
analyst
▴ 30
Resolved by increasing heapsize of -Xmx50G
Comment: STAR aligner error
by
Ram
43k
Talk to your HPC sysadmin - array jobs might be getting different kinds of nodes compared to standalone jobs.
Comment: Is therer any suggestions on mapping rate of WGBS data?
by
Zeng Jingyu
▴ 60
Thank you for your answer!
Answer: HCL database download
by
sooni
▴ 20
I solved the problem by conneting another internet exploer. I think it was probably a problem with Chrome itself.
Answer: barcode of TCR-sequencing
by
mizraelson
▴ 60
Hi, What protocol did you use for TCR-seq library preparation? Generally speaking, there is no need to remove barcodes, as MiXCR can work …
Comment: Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, C
by
qwertyuiop26
• 0
I've implemented fm index with backward search and need an inexact search to implement on FM index, I couldn't understand how fm index coul…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 400
The md5 hash they refer to on line 22 (f46a7ca244afef522b22a11bd33d27b1) appears to map to a *S. aureus* strain, not *S. hominis* (you can …
Comment: Correlating Bulk Differential Expression with quantitative
by
Qroid
▴ 40
You could try including disease scale for each sample as a design factor. See the vignette here https://bioconductor.org/packages/devel/bio…
Comment: Help with generating annotation database for dog genome to use in ANNOVAR for v
by
sainavyav22
• 0
Hello, Thanks for the reply. I could only see the refMrna.fa file in the link you provided. Where can I get the refGene.txt file. Thanks fo…
Answer: Understanding STAR output (Aligned.out.sam file)
by
heelpPlease
• 0
After thoroughly reviewing all the documents again, I've identified the root cause of my initial issue: the failure to detect essential gen…
Comment: Understanding STAR output (Aligned.out.sam file)
by
heelpPlease
• 0
Thank you! Now that I understand that there is a difference between read and fragment, I could actually find a lot of helpful information..…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
sovrappensiero
▴ 90
Thanks again. Hmm...this makes me suspicious of whether this normalization is actually possible. In case you'd like to take a look, [here]…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
Jeremy Leipzig
22k
The seven genotypes being 58025AA, 58025AG, 58051TT, 58051TC, 58051CC, 58057TT, 58057TC
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