Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this week
all time
today
this week
this month
this year
172 results • Page
2 of 4
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
136
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
3 days ago by
Javier
• 0
0
votes
1
reply
227
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 2 days ago by
Thanujay S
• 0 • written 3 days ago by
yahn
• 0
0
votes
0
replies
129
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
3 days ago by
mikemakaveli1
• 0
2
votes
2
replies
208
views
Raw counts using stringtie
stringtie
RNA-seq
updated 3 days ago by
GenoMax
142k • written 3 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
128
views
Modify plot R mtDNA indel
plot
mtDNA
R
3 days ago by
marco.barr
▴ 90
0
votes
0
replies
252
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
3 days ago by
NorbertK
• 0
2
votes
2
replies
218
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 2 days ago by
Ram
43k • written 3 days ago by
carolofharvest
▴ 30
10
votes
10
replies
609
views
High Malat-1 expression in single cell data
single-cell
updated 7 hours ago by
t.montserrat.ayuso
▴ 10 • written 7 days ago by
carolofharvest
▴ 30
0
votes
2
replies
240
views
Downloading older version of a tool
Alignment
tools
2 days ago by
Ruqaiya
• 0
0
votes
0
replies
145
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
3 days ago by
rustykb
▴ 20
1
vote
1
reply
178
views
DSEQ2 analysis
DESEQ2
logfoldchange
updated 2 days ago by
Ram
43k • written 3 days ago by
adi.gershon1
• 0
3
votes
5
replies
269
views
Generating mpileup file using samtools
mpileup
samtools
updated 3 days ago by
Joe
21k • written 3 days ago by
Ruqaiya
• 0
0
votes
5
replies
343
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 3 days ago by
b.contreras.moreira
▴ 180 • written 4 days ago by
JH
• 0
1
vote
3
replies
282
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 3 days ago by
ATpoint
82k • written 3 days ago by
Qi
• 0
0
votes
0
replies
135
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
3 days ago by
Amos Bairoch
▴ 120
2
votes
3
replies
273
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 3 days ago by
dthorbur
★ 1.9k • written 3 days ago by
Vijith
▴ 30
0
votes
0
replies
144
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
3 days ago by
Jeyong
• 0
0
votes
2
replies
728
views
homer not configured properly
Homer
makeTagDirectory
updated 3 days ago by
clairechung112
• 0 • written 23 months ago by
amahdi779
• 0
1
vote
3
replies
253
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 3 days ago by
Alex Reynolds
35k • written 3 days ago by
SJP
• 0
0
votes
0
replies
132
views
Empty table plot using plotGseaTable()
FGSEA
2 days ago by
Chris
▴ 260
0
votes
1
reply
179
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 3 days ago by
anovak
▴ 120 • written 4 days ago by
Hang
• 0
1
vote
3
replies
234
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 3 days ago by
jared.andrews07
★ 16k • written 4 days ago by
yvonneh
▴ 10
3
votes
5
replies
310
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
3 days ago by
Maverick
▴ 10
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 4 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
190
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
4 days ago by
dtnondorf
• 0
0
votes
3
replies
239
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 27 minutes ago by
Chris Dean
▴ 390 • written 4 days ago by
sovrappensiero
▴ 90
1
vote
2
replies
235
views
RNA-seq data for deep learning classification
rna-seq
3 days ago by
yahn
• 0
2
votes
8
replies
434
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
15 minutes ago by
Qroid
▴ 40
0
votes
1
reply
510
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 4 days ago by
Hugo
• 0 • written 4 months ago by
Rachel
• 0
0
votes
1
reply
148
views
Provean help
variant
Provean
updated 4 days ago by
Mensur Dlakic
★ 27k • written 4 days ago by
Arun Sai Kumar
• 0
1
vote
1
reply
163
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated 4 days ago by
bk11
★ 2.4k • written 4 days ago by
Jeol
▴ 20
1
vote
1
reply
170
views
Super ehancers
enhancers
updated 4 days ago by
jared.andrews07
★ 16k • written 4 days ago by
Oburah
• 0
0
votes
6
replies
292
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
updated 3 days ago by
dsull
★ 6.0k • written 4 days ago by
Chen
• 0
5
votes
5
replies
277
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 4 days ago by
atharvakarkare14
▴ 30 • written 4 days ago by
Begonia_pavonina
▴ 150
1
vote
7
replies
440
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
3 days ago by
eebloom
▴ 80
3
votes
3
replies
323
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression
RNA
NOISeq
DGE
updated 3 days ago by
ATpoint
82k • written 4 days ago by
alifafiq1
• 0
0
votes
0
replies
100
views
Use of annotation of integrated Seurat object in single sample
Seurat
4 days ago by
Bine
▴ 60
0
votes
0
replies
106
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 4 days ago by
Ram
43k • written 4 days ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
225
views
Subsetting and merging back Seurat Object brings different results
Seurat
4 days ago by
Bine
▴ 60
0
votes
0
replies
138
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
NGS
Genomics
Post-doc
R-loops
updated 4 days ago by
Ram
43k • written 4 days ago by
4r-rtg
• 0
1
vote
1
reply
138
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 4 days ago by
Ram
43k • written 4 days ago by
marco.barr
▴ 90
0
votes
0
replies
96
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
4 days ago by
Vijith
▴ 30
9
votes
10
replies
510
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 4 days ago by
Zamin Iqbal
▴ 20 • written 5 days ago by
nicole.kavanagh
• 0
0
votes
1
reply
277
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 4 days ago by
Scooter
▴ 280 • written 11 days ago by
avocado123
• 0
0
votes
0
replies
96
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
4 days ago by
James
▴ 10
0
votes
1
reply
586
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 4 days ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
1
vote
3
replies
235
views
Odd alignment question/finding
Alignment
updated 3 days ago by
barslmn
★ 2.1k • written 4 days ago by
poordumbsillyidiot
• 0
0
votes
1
reply
207
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 4 days ago by
GenoMax
142k • written 4 days ago by
mgranada3
▴ 30
0
votes
0
replies
98
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
4 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 4 days ago by
Ram
43k • written 4 days ago by
Oscar
▴ 10
172 results • Page
2 of 4
Recent Votes
Answer: Gene ontology and homologs
Comment: anRichment is missing
Comment: Gene Specific coverage from WGS data
Comment: Gene Specific coverage from WGS data
Comment: High Malat-1 expression in single cell data
A: Meme-Tools: Bit score
Meme-Tools: Bit score
Recent Locations •
All
United Kingdom,
2 minutes ago
United States,
2 minutes ago
United States,
2 minutes ago
United States,
3 minutes ago
Japan,
3 minutes ago
Bologna,
4 minutes ago
Whitefish, MT,
4 minutes ago
Recent Awards •
All
Popular Question
to
JACKY
▴ 140
Popular Question
to
bhumm
▴ 140
Teacher
to
Matthias Zepper
4.6k
Popular Question
to
sidrah.maryam
▴ 50
Popular Question
to
gubrins
▴ 290
Popular Question
to
arshad1292
▴ 100
Popular Question
to
ahmad mousavi
▴ 800
Recent Replies
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
▴ 40
Thank you. Maybe it's best to confirm with the authors about how they're getting responder/non-responder labels. I'll do that now.
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 390
If you sequenced a short hypervariable region, most of your sequence reads will not be able to be assigned to the species level. One possi…
Comment: anRichment is missing
by
GenoMax
142k
Consider emailing Dr. Horvath about this. Until enough people make him aware of this issue WGCNA "problem" is unlikely to get fixed.
Comment: anRichment is missing
by
Tatyana
• 0
Unfortunately, there are only tutorials and codes for tutorials for WGCNA, not installation files for any their packages... :(
Comment: anRichment is missing
by
GenoMax
142k
See this link for the WGCNA documentation and code from Peter Langfelder : https://bioinformatics.stackexchange.com/questions/21885/where-t…
Comment: anRichment is missing
by
Tatyana
• 0
The problem is back, Horwath's lab web is down again. Is it possible to get anRichment istallation file somewhere? (The greater problem is …
Comment: 16S rRNA microbiome differential abundance analysis with DESeq2 finds same micro
by
andres.firrincieli
3.6k
1. Maribaculaceae is a family not a genus 2. Who said that ASV with the same taxonomic classification must have the same behaviour? 3. With…
Comment: Question regarding WGCNA
by
andres.firrincieli
3.6k
the within-group variability is so small that these look like technical replicates rather than independent biological replicates
Answer: Gene ontology and homologs
by
geneontologyhelp
▴ 400
No. Homology is defined as shared common ancestry. Two genes that take part in the same biological process may not have the same functio…
Answer: error in R code
by
Matthias Zepper
4.6k
I quickly googled [the source code of that function][1], and the error is triggered by this condition: if(length(wn) < 1 || !is.whol…
Comment: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
by
kalavattam
▴ 190
Thanks for the explanation. I noticed and corrected a typo in which "*read* reverse strand" initially read as "*mate* reverse strand" in t…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
sovrappensiero
▴ 90
It's a commercial product, a *Staphylococcus hominis* genome. This species is not found in the DADA2 results, so I guess DADA2 is not ident…
Comment: Question regarding WGCNA
by
Ram
43k
Plots are incomplete without legends. Please share the complete plot with mappings for shape and color.
Comment: Quetion regarding WGCNA
by
deepak
• 0
Thank you for your reply andres.firrincieli. I have attached the PCA plot of the expression data used in the WGCNA. ![enter imag…
Comment: Design matrix Differential expression analysis
by
SHN
▴ 40
Got it, thank you for your response. SN
Traffic: 2551 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