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 year
all time
today
this week
this month
this year
1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
2
replies
274
views
Modify the code to take most abundant reads from a cluster and process it.
cd-hit-est
clustering
5 days ago by
Mo
▴ 40
1
vote
2
replies
245
views
Understanding TCGA barcodes with dot in the fieldname
tcga
updated 2 days ago by
Zhenyu Zhang
▴ 980 • written 5 days ago by
Tahsin
• 0
0
votes
0
replies
157
views
Compare peaks between clusters in sc-ATAC
Peak-Calling
Epigenome
scATAC-seq
updated 5 days ago by
Ram
40k • written 5 days ago by
Ahmed.waraky
▴ 10
0
votes
4
replies
570
views
Weirdness in annotation (missing allele frequencies)
allele-frequency
gnomad
annovar
updated 4 days ago by
Jeremy Leipzig
21k • written 6 days ago by
Can Abdullah
• 0
1
vote
3
replies
232
views
Finding sequences in unannotated genomes using reference coordinates
consensus
VCF
updated 6 days ago by
Ram
40k • written 6 days ago by
Prangan
▴ 20
0
votes
1
reply
217
views
High amount of intronic/intergenic reads in SMARTer stranded total bulk RNAseq
RNA-seq
DNA
SMARTer
updated 6 days ago by
Ram
40k • written 6 days ago by
Mat
▴ 60
0
votes
0
replies
342
views
Why dbConnect GEOmetadb_demo.sqlite shows some information while dbConnect GEOmetadb.sqlite shows no information
R
GEO
GEOmetadb
updated 6 days ago by
Pierre Lindenbaum
157k • written 6 days ago by
nonaddldy
▴ 10
1
vote
5
replies
359
views
ATAC-seq troubleshoot - Just Noise
ATAC-seq
updated 2 days ago by
ATpoint
77k • written 6 days ago by
vk
▴ 40
0
votes
0
replies
173
views
High pvalues when using clusterProfiler for seurat
clusterProfiler
6 days ago by
Ahmed
• 0
5
votes
7
replies
424
views
Salmon index not progressing
salmon
updated 6 days ago by
Michael
53k • written 6 days ago by
camillab.
▴ 140
0
votes
0
replies
166
views
scanpy problem for empty cells
scanpy
updated 6 days ago by
Ram
40k • written 6 days ago by
Andy
▴ 90
0
votes
0
replies
170
views
Current landscape of approaches to scRNA-seq with nanopore sequencers?
scRNA-seq
nanopore
single-cell
4 days ago by
LauferVA
3.7k
0
votes
1
reply
211
views
How to download genomes and proteins from JGI in bulk via the command line?
jgi
cli
updated 6 days ago by
Ram
40k • written 7 days ago by
O.rka
▴ 680
0
votes
5
replies
449
views
genome data downloads for various strains
gisaid
hass-marr
updated 3 days ago by
Ram
40k • written 7 days ago by
iftikharmaryam123
• 0
0
votes
0
replies
183
views
Illumina methylation EPIC V2 array
ewas
methylation
enrichment
missMethyl
EPIC
7 days ago by
juliviglino
• 0
0
votes
1
reply
205
views
Esearch, Epost, and Efetch for Large Datasets in Biopython
eutils
biopython
entrez
updated 7 days ago by
Ram
40k • written 8 days ago by
Salem
• 0
3
votes
10
replies
512
views
STAR index not working
STAR
RNA-Seq
6 days ago by
camillab.
▴ 140
2
votes
3
replies
285
views
Can I infer the fraction of replicating cells from bulk RNA-seq data?
replication
apoptosis
updated 8 days ago by
Ram
40k • written 8 days ago by
txema.heredia
▴ 80
0
votes
1
reply
166
views
Prank checkpoint and restore?
prank
alignment
updated 8 days ago by
Ram
40k • written 8 days ago by
Pit
• 0
0
votes
13
replies
577
views
STAR Intron Motif Script Gives Segmentation fault Error
STAR
Linux
5 days ago by
Y
• 0
1
vote
3
replies
247
views
Sub-sampleing bam files based on sequencing_summary.txt (guppy output)
samtools
guppy
updated 8 days ago by
GenoMax
134k • written 8 days ago by
anika.john
• 0
0
votes
0
replies
120
views
Any way to predict hormone biosynthesis pathways in understudied organisms?
genomics
orthologs
biosynthesis-pathway
updated 8 days ago by
Ram
40k • written 8 days ago by
Mark
• 0
2
votes
4
replies
323
views
Refseq annotation | Populus trichocarpa
R
RNA-seq
plants
Refseq
updated 8 days ago by
Ram
40k • written 8 days ago by
P
• 0
1
vote
1
reply
200
views
Read Counts from BAM file
bam
samtools
qualimap
readcount
updated 8 days ago by
ATpoint
77k • written 8 days ago by
Smriti
• 0
0
votes
2
replies
237
views
Is it okay to just average the log2FC values across different cell types in pseudobulk scRNA-seq data?
scrna-seq
rna-seq
log2fc
8 days ago by
JLee
• 0
0
votes
1
reply
192
views
Identify parent of each read in a GAF
gaf
vgteam
vg
updated 8 days ago by
Jordan M Eizenga
▴ 360 • written 9 days ago by
cfourps
▴ 10
0
votes
3
replies
260
views
Errors while trying to run Scenic
Scenic
updated 9 days ago by
GenoMax
134k • written 9 days ago by
Stavroula
• 0
0
votes
3
replies
272
views
How to find target genes From RNA seq data?
Cotton
DGE
RNA-seq
updated 9 days ago by
Ram
40k • written 9 days ago by
Fizzah
▴ 30
0
votes
0
replies
138
views
maftools - median survival time doesn't match plot
R
survival
maftools
K-M
9 days ago by
BioGuy
• 0
0
votes
1
reply
174
views
vg rna pantranscriptome
rna
vg
updated 9 days ago by
Jordan M Eizenga
▴ 360 • written 9 days ago by
z
• 0
0
votes
0
replies
129
views
Genetic distance in cM from VCF of non-reference species to run Beagle
plink
beagle
vcf
updated 9 days ago by
Ram
40k • written 9 days ago by
AndrMod
• 0
1
vote
4
replies
304
views
rRNA filtering from human RNA-seq data
rRNA
RNA-seq
9 days ago by
deniz
▴ 10
0
votes
5
replies
363
views
manhattan plot with vcf information
R
manhattan
vcf
updated 7 days ago by
dthorbur
▴ 550 • written 9 days ago by
sooni
▴ 10
0
votes
0
replies
551
views
after gatk VariantAnnotator -V *_com_norm.vcf -A AlleleFraction -O *_norm_AB.vcf There "nan,nan" or "nan" in my vcf file
gatk
AlleleFraction
VariantAnnotator
updated 9 days ago by
Ram
40k • written 9 days ago by
zhuo
• 0
2
votes
0
replies
142
views
the dispersion estimation of edgeR and DESeq2
estimation
dipersion
edgeR
DESeq2
9 days ago by
tommy
▴ 30
2
votes
3
replies
299
views
Genewise output help
genewise
updated 9 days ago by
Jean-Karim Heriche
26k • written 9 days ago by
lorenzoedg
• 0
2
votes
1
reply
180
views
Best Tools and Practices for CNV Variant Calling in WES Data
CNV
WES
updated 10 days ago by
Pierre Lindenbaum
157k • written 10 days ago by
Nadav
▴ 10
0
votes
2
replies
201
views
Identify genes for mapped reads with combined human-7HPV genome index
star
samtools
updated 10 days ago by
Ram
40k • written 10 days ago by
r.j.lock
• 0
0
votes
0
replies
128
views
Data for pathview() (KEGG Pathway Map) after EdgeR
EdgeR
LogFC
pathview
KEGG
10 days ago by
Ann
▴ 10
0
votes
0
replies
276
views
GTF/Reference genome adjustments? Gene-based differential expression analysis of genetically modified mouse line
RNA-seq
DGE
updated 10 days ago by
Ram
40k • written 10 days ago by
alex
• 0
0
votes
0
replies
147
views
Selecting SNPs for two-sample Mendelian randomization study/analysis
Two-sample
SNPs
Mendelian
randomization
10 days ago by
huynguyenacademia
• 0
0
votes
0
replies
142
views
cosine simialrity of mutation signature analysis
similarity
Mutational
analysis
signature
cosine
10 days ago by
probioquestioner
• 0
0
votes
1
reply
220
views
Significance testing of top vs. random SNPs
SNPs
significance
variance
statistical
updated 7 days ago by
dthorbur
▴ 550 • written 10 days ago by
am29
▴ 30
4
votes
2
replies
439
views
Recommended way to normalize SmartSeq2 gene expression matrix to better match 10X expression data
rna-seq
smartseq2
r
updated 8 days ago by
yhdist
▴ 70 • written 10 days ago by
Cookin
▴ 10
0
votes
0
replies
152
views
Why we are using filtering >0 for up and <0 for down after TopTags() to extract de genes ids?
EdgeR
logfc
DEG
11 days ago by
Ann
▴ 10
0
votes
1
reply
179
views
PyMOL: how to list all selection names?
pymol
updated 10 days ago by
Wayne
★ 1.8k • written 11 days ago by
Ondina
▴ 90
2
votes
2
replies
221
views
Clustering algorithm based on grouping sequences into gene families
gene-families
clustering
updated 10 days ago by
Ram
40k • written 11 days ago by
francesco
• 0
0
votes
0
replies
146
views
Homozygous reference genotype for a GIAB genome
GIAB
IDs
reference
rs
Homozygous
11 days ago by
New2R
▴ 60
0
votes
0
replies
150
views
PRSice - Phenotype File Not Read Correctly
PRSice2
11 days ago by
V
• 0
0
votes
2
replies
1.6k
views
Question about REDItools
REDItools
updated 12 days ago by
Ethan Lee
• 0 • written 4.1 years ago by
tujuchuanli
▴ 100
1,000 results • Page
2 of 20
Recent Votes
C: How Do I Convert Fa Files To Bed Format?
Clustering in single cell
Answer: Network analysis with cytoscape
Answer: Network analysis with cytoscape
Network analysis with cytoscape
Comment: How to convert data in r?
Comment: Frustrated with DEA results
Recent Locations •
All
United Kingdom,
1 minute ago
Stony Brook University, NY,
2 minutes ago
Ithaca,
2 minutes ago
India,
5 minutes ago
EMBL Heidelberg, Germany,
6 minutes ago
germany,
7 minutes ago
United States,
8 minutes ago
Recent Awards •
All
Scholar
to
rfran010
▴ 830
Popular Question
to
Alexander
▴ 200
Popular Question
to
Matteo Schiavinato
★ 3.6k
Commentator
to
Michael Love
★ 2.5k
Teacher
to
PavolG
▴ 30
Great Question
to
xqyn
• 0
Scholar
to
GenoMax
134k
Recent Replies
Comment: How to subset large BAM files specifically/ extract specific subsets?
by
ella
• 0
I think I even used `reformat.sh` earlier today, but don´t remember with what arguments. I now tried what you suggested, but got an error: …
Comment: Clustering in single cell
by
Jean-Karim Heriche
26k
Are you doing the clustering in UMAP space? If so, avoid distance-based clustering because distances are only meaningful locally, i.e dista…
Comment: Github access with token headache
by
Ram
40k
Yes please.
Comment: How to convert data in r?
by
Ram
40k
> tidyr does not make anything tidy at all I don't get your point. The code does not use tidyr (`%>%` is from `magrittr`) and there is no …
Comment: Unmapped Reads in Kallisto
by
GenoMax
134k
https://www.biostars.org/u/30020/ you can add a solution to this thread. It looks like this poster has a similar issue described in origina…
Comment: Unmapped Reads in Kallisto
by
dsull
★ 4.7k
Create a new thread if you need help with this.
Comment: Network analysis with cytoscape
by
Chris
▴ 200
Thanks xanderpico! That is great resources. There are many bioinformatics tools now which is hard to choose an appropriate one. I found thi…
Comment: Frustrated with DEA results
by
dsull
★ 4.7k
Great suggestion on visualizing the data as well as doing DE between variables that you know should result in different gene expression pro…
Answer: Network analysis with cytoscape
by
xanderpico
▴ 500
Hi Chris. There are dozens of different directions you could go using Cytoscape. There is not just one analysis path. You mention "tran…
Comment: How to convert data in r?
by
Jeremy
▴ 840
Great answer bk11. star, you'll need the dplyr package to run this code. Just make the following the first line of code: library(dpl…
Comment: Troubles launch IGV on Linux(Debian)
by
PoscaXVIII
• 0
Hi barslmn, Thank you so much for your help it works perfectly. No more frozen black screen. I just changed from wayland to Xorg (On the pa…
Comment: Complex multifactorial DE analysis with limma/edgeR based on rnaseq data
by
LChart
3.4k
> I tried a general "overall" group comparison of the "general" conditions, trying to model the "donor" effect and including it into the de…
Comment: How to convert data in r?
by
Kevin Blighe
86k
Funny how *tidyr* does not make anything tidy at all. Why not just use (actually less characters): data <- data.frame(c( "A \t 22…
Comment: Frustrated with DEA results
by
Jeremy Leipzig
21k
If the FDR is killing your results, it's ok to filter out genes that are not informative https://www.bioconductor.org/help/course-materials…
Comment: Github access with token headache
by
Begonia_pavonina
▴ 110
I will post it in StackOverflow, should I delete this thread?
Traffic: 1855 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