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 month
all time
today
this week
this month
this year
901 results • Page
6 of 19
Sort: Rank
Rank
Views
Votes
Replies
1
vote
2
replies
1.2k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
10 days ago by
Zhenyu Zhang
★ 1.2k
2
votes
1
reply
328
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 12 days ago by
chrchang523
10k • written 15 days ago by
8armed
▴ 10
0
votes
5
replies
377
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 12 days ago by
chrchang523
10k • written 12 days ago by
curious
▴ 750
0
votes
1
reply
229
views
visualize GSEA
barplot
RNA-seq
GSEA
enrichment
updated 11 days ago by
Ram
43k • written 12 days ago by
Rob
▴ 170
0
votes
2
replies
268
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 5 days ago by
GenoMax
142k • written 12 days ago by
Ximena
• 0
0
votes
1
reply
212
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 12 days ago by
Ram
43k • written 12 days ago by
Valentina
• 0
0
votes
6
replies
470
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 12 days ago by
swbarnes2
14k • written 12 days ago by
Erina
• 0
1
vote
3
replies
319
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
10 days ago by
Lada
▴ 30
1
vote
0
replies
154
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 9 days ago by
zx8754
11k • written 12 days ago by
Emilie
▴ 10
0
votes
0
replies
143
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
12 days ago by
Javier
• 0
0
votes
2
replies
294
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 3 days ago by
Zhenyu Zhang
★ 1.2k • written 12 days ago by
yahn
• 0
0
votes
0
replies
135
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
12 days ago by
mikemakaveli1
• 0
2
votes
2
replies
240
views
Raw counts using stringtie
stringtie
RNA-seq
updated 12 days ago by
GenoMax
142k • written 12 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
135
views
Modify plot R mtDNA indel
plot
mtDNA
R
12 days ago by
marco.barr
▴ 120
0
votes
0
replies
332
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
12 days ago by
NorbertK
▴ 10
4
votes
2
replies
263
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 11 days ago by
Ram
43k • written 12 days ago by
carolofharvest
▴ 40
13
votes
14
replies
895
views
High Malat-1 expression in single cell data
single-cell
updated 7 days ago by
t.montserrat.ayuso
▴ 40 • written 16 days ago by
carolofharvest
▴ 40
0
votes
2
replies
278
views
Downloading older version of a tool
Alignment
tools
12 days ago by
Ruqaiya
• 0
0
votes
0
replies
155
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
12 days ago by
rustykb
▴ 20
1
vote
1
reply
202
views
DSEQ2 analysis
DESEQ2
logfoldchange
updated 11 days ago by
Ram
43k • written 12 days ago by
adi.gershon1
• 0
3
votes
5
replies
327
views
Generating mpileup file using samtools
mpileup
samtools
updated 12 days ago by
Joe
21k • written 12 days ago by
Ruqaiya
• 0
0
votes
5
replies
409
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 12 days ago by
b.contreras.moreira
▴ 180 • written 13 days ago by
JH
• 0
1
vote
3
replies
305
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 12 days ago by
ATpoint
82k • written 13 days ago by
Qi
• 0
0
votes
0
replies
146
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
12 days ago by
Amos Bairoch
▴ 120
2
votes
3
replies
319
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 12 days ago by
dthorbur
★ 2.0k • written 12 days ago by
Vijith
▴ 30
0
votes
0
replies
160
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
13 days ago by
Jeyong
• 0
0
votes
2
replies
744
views
homer not configured properly
Homer
makeTagDirectory
updated 13 days ago by
clairechung112
• 0 • written 24 months ago by
amahdi779
• 0
1
vote
3
replies
301
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 13 days ago by
Alex Reynolds
35k • written 13 days ago by
SJP
• 0
0
votes
0
replies
146
views
Empty table plot using plotGseaTable()
FGSEA
12 days ago by
Chris
▴ 280
0
votes
1
reply
205
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 13 days ago by
anovak
▴ 120 • written 13 days ago by
Hang
• 0
1
vote
3
replies
263
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 13 days ago by
jared.andrews07
★ 16k • written 13 days ago by
yvonneh
▴ 10
3
votes
5
replies
375
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
12 days ago by
Maverick
▴ 10
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 13 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
228
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
13 days ago by
dtnondorf
• 0
3
votes
8
replies
676
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 9 days ago by
Chris Dean
▴ 410 • written 13 days ago by
sovrappensiero
▴ 100
1
vote
2
replies
267
views
RNA-seq data for deep learning classification
rna-seq
12 days ago by
yahn
• 0
3
votes
8
replies
571
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
9 days ago by
Qroid
▴ 40
0
votes
1
reply
535
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 13 days ago by
Hugo
• 0 • written 5 months ago by
Rachel
• 0
0
votes
1
reply
173
views
Provean help
variant
Provean
updated 13 days ago by
Mensur Dlakic
★ 27k • written 13 days ago by
Arun Sai Kumar
• 0
1
vote
1
reply
180
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated 13 days ago by
bk11
★ 2.4k • written 14 days ago by
Jeol
▴ 20
1
vote
1
reply
187
views
Super ehancers
enhancers
updated 13 days ago by
jared.andrews07
★ 16k • written 13 days ago by
Oburah
• 0
4
votes
7
replies
392
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
2 days ago by
Chen
• 0
5
votes
5
replies
311
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 13 days ago by
atharvakarkare14
▴ 30 • written 13 days ago by
Begonia_pavonina
▴ 150
1
vote
7
replies
484
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
12 days ago by
eebloom
▴ 80
3
votes
3
replies
361
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 12 days ago by
ATpoint
82k • written 13 days ago by
alifafiq1
• 0
0
votes
0
replies
106
views
Use of annotation of integrated Seurat object in single sample
Seurat
13 days ago by
Bine
▴ 60
0
votes
0
replies
115
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 13 days ago by
Ram
43k • written 13 days ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
249
views
Subsetting and merging back Seurat Object brings different results
Seurat
13 days ago by
Bine
▴ 60
0
votes
0
replies
173
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
NGS
Genomics
Post-doc
R-loops
updated 13 days ago by
Ram
43k • written 13 days ago by
4r-rtg
• 0
1
vote
1
reply
156
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 13 days ago by
Ram
43k • written 13 days ago by
marco.barr
▴ 120
901 results • Page
6 of 19
Recent Votes
A: ensembl gene id
A: How to deal with the case that one gene symbol matches multiple ensembl ids?
Answer: DESeq2 error
Answer: Using ggplotly in R
Comment: How to calculate coverage of Nanopore long read data?
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Calculate allelic frequency from VEP output vcf file
Recent Locations •
All
Australia,
2 minutes ago
Pakistan,
2 minutes ago
United States,
3 minutes ago
Bologna,
5 minutes ago
Singapore,
7 minutes ago
Russia,
10 minutes ago
Spain,
12 minutes ago
Recent Awards •
All
Scholar
to
ramiro.barrantes
• 0
Popular Question
to
AshleeThomson
▴ 80
Popular Question
to
vk
▴ 10
Scholar
to
Prawesh
• 0
Popular Question
to
Jean-Karim Heriche
27k
Popular Question
to
Chironex
▴ 40
Scholar
to
rpolicastro
13k
Recent Replies
Answer: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
by
kuttibiotech2009
▴ 30
Hello friends, Thank you for your feedback. I understand that the post may not directly relate to bioinformatics. My aim was to share …
Comment: how to treat the replicates while performing WGCNA
by
andres.firrincieli
3.6k
You do not merge the MEs. It is quite normal that some modules have noisy eigengenes (MEs); WGCNA is an unsupervised analysis overall. By …
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
my blast is latest version 2.15. I don't know what you want me to see in this link.
Answer: scRNAseq quality control weird double curve in nFeature vs nCount plot
by
valdirbarth
▴ 20
Is it possible that the cells that have their VDJ sequenced, those VDJ reads are not contributing to new genes detected? So you might be …
Comment: ggrepel function: geom_text_repel()
by
ntsopoul
▴ 60
The plot looks confusing, chek the documentation there is an attribute called force. If you reduce the value you should get better results.…
Comment: Sequencing Depth (Read Depth) Calculations
by
LucisTheFather
• 0
Understood! Gonna try those two!
Comment: Sequencing Depth (Read Depth) Calculations
by
LucisTheFather
• 0
Thank u very much!
Comment: How to extract cells of different species after mapping with combined genome?
by
GenoMax
142k
You have used the tag `snRNAseq`. I am not familiar with singleron tech but if you have sequence data you may be able to use `xenome` or `b…
Comment: bbmerge (bbmap) ~ error with insert size file output
by
GenoMax
142k
It may be best to go back to the original data and then do `bbmerge.sh` on it to get original insert size estimates (before any operations …
Comment: bbmerge (bbmap) ~ error with insert size file output
by
chrisk
• 0
Hi Brian, Thank you and apologies for the extra future revision works. Out of curiosity we disabled neural networks 'nn=f' and the file o…
Comment: bbmerge (bbmap) ~ error with insert size file output
by
chrisk
• 0
Hi Genomax, This is the thread: https://www.biostars.org/p/9582467/ Cheers, Chris
Comment: Inquiry about deseq2 transformation
by
Chen
• 0
that's helpful, thanks :)
Comment: bbmerge (bbmap) ~ error with insert size file output
by
Brian Bushnell
20k
Ah, this is a little embarrassing; those are the vectors for the neural network. I overloaded a field that was being used for the insert s…
Comment: Annotating file using bcftools
by
kl
▴ 10
Thanks - I corrected it. It doesn't seem to annotate. I converted to binary after which is what is shown below. It is not the output I want…
Comment: Filtering VCF files based on VAF giving incorrect results
by
Arton
▴ 10
These are valid questions. Does your code address the concerns you've raised? From what I understand, FilterVcf is primarily designed for h…
Traffic: 1704 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