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
400 results • Page
5 of 8
Sort: replies
Rank
Views
Votes
Replies
0
votes
1
reply
207
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 4 days ago by
ATpoint
82k • written 4 days ago by
Amr
▴ 160
0
votes
1
reply
184
views
unable to get feature count results
featureCounts
updated 14 days ago by
Ram
43k • written 14 days ago by
Ravita
• 0
0
votes
1
reply
416
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 26 days ago by
Ram
43k • written 20 months ago by
Muhammad
• 0
1
vote
1
reply
209
views
Failed kmer content
kmer
illumina
ngs
updated 21 days ago by
Ram
43k • written 21 days ago by
Kasturi
• 0
0
votes
1
reply
146
views
consensus sequence calling
consensus
updated 1 day ago by
bk11
★ 2.4k • written 1 day ago by
Ghada
• 0
0
votes
1
reply
2.8k
views
Can't make sva comparison despite very distinct batch effects
sva
batch-effect
updated 27 days ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
0
votes
1
reply
529
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 19 days ago by
ginellegrenier
• 0 • written 5 months ago by
Clayton
• 0
1
vote
1
reply
2.7k
views
Plotting a PCA Plot from SVASeq results
pca
ruvseq
sva
svaseq
batch-effect
updated 28 days ago by
Ram
43k • written 6.3 years ago by
jjrin
▴ 40
0
votes
1
reply
271
views
creating batch colum for batch correction
batch-correction
combat
8 days ago by
Expert
▴ 10
0
votes
1
reply
192
views
Differential Accessibility
DiffBind
updated 15 days ago by
Ram
43k • written 15 days ago by
Shloka
• 0
1
vote
1
reply
154
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 5 days ago by
andres.firrincieli
3.6k • written 5 days ago by
kacollier
▴ 30
0
votes
1
reply
204
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 21 days ago by
GenoMax
142k • written 21 days ago by
Srinka
▴ 20
1
vote
1
reply
445
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 5 days ago by
Jaïr
• 0 • written 4 months ago by
NorbertK
▴ 10
0
votes
1
reply
170
views
Provean help
variant
Provean
updated 12 days ago by
Mensur Dlakic
★ 27k • written 12 days ago by
Arun Sai Kumar
• 0
0
votes
1
reply
183
views
Microbial Signal Transduction Database
MiST
updated 4 days ago by
zx8754
11k • written 4 days ago by
Shravani
• 0
0
votes
1
reply
156
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 6 days ago by
Bastien Hervé
5.3k • written 7 days ago by
sooni
▴ 20
0
votes
1
reply
198
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 13 days ago by
i.sudbery
19k • written 14 days ago by
Edmond
• 0
0
votes
1
reply
179
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 4 days ago by
GenoMax
142k • written 4 days ago by
maria.soler
• 0
0
votes
1
reply
188
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 21 days ago by
Mensur Dlakic
★ 27k • written 21 days ago by
benguyarenbeyaz98
• 0
0
votes
1
reply
697
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 14 days ago by
Ram
43k • written 14 days ago by
Dr Huma Naz
• 0
0
votes
1
reply
319
views
Could you please assist in identifying this cluster?
single-cell
updated 25 days ago by
Ram
43k • written 25 days ago by
carolofharvest
▴ 40
1
vote
1
reply
1.7k
views
sea corrected expression matrix
sva
microarrays
batch-effect
updated 27 days ago by
Ram
43k • written 6.8 years ago by
ATCG
▴ 380
0
votes
1
reply
93
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
updated 11 hours ago by
GenoMax
142k • written 12 hours ago by
melissa.joubert
• 0
0
votes
1
reply
104
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
updated 9 hours ago by
GenoMax
142k • written 9 hours ago by
bioinfo
▴ 150
1
vote
1
reply
102
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 10 hours ago by
Ram
43k • written 15 hours ago by
kilcdincer
▴ 10
0
votes
1
reply
137
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 1 day ago by
GenoMax
142k • written 1 day ago by
cedric.blais
• 0
0
votes
1
reply
1.3k
views
About BatchQC packages error
Batch-effect
R
updated 27 days ago by
Ram
43k • written 6.1 years ago by
Jun
• 0
0
votes
1
reply
214
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 4 days ago by
curious
▴ 750 • written 4 days ago by
SeoGyun
• 0
0
votes
1
reply
145
views
input file for alternative splicing in rmats in linux
rmats
updated 5 days ago by
Ram
43k • written 5 days ago by
Lambodarswain316
• 0
0
votes
1
reply
259
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 7 days ago by
GenoMax
142k • written 7 days ago by
Sony
▴ 10
1
vote
1
reply
250
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 14 days ago by
Ram
43k • written 14 days ago by
Jonathan Yoou
▴ 60
0
votes
0
replies
1.5k
views
minifi for RRBS
rrbs
batch-effect
methylation
updated 28 days ago by
Ram
43k • written 7.2 years ago by
German.M.Demidov
★ 2.9k
0
votes
0
replies
99
views
monocle 3-- Could not get node in small cluster
monocle3
7 days ago by
synat.keam
▴ 100
0
votes
0
replies
135
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 14 days ago by
Ram
43k • written 14 days ago by
Alexandros
• 0
0
votes
0
replies
107
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
13 days ago by
James
▴ 10
0
votes
0
replies
195
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
27 days ago by
Ali
• 0
0
votes
0
replies
124
views
How to implement an IGV to streamlit app?
python
streamlit
igv
8 days ago by
avigail.shnaider
• 0
0
votes
0
replies
167
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames
RNA-Seq
WGCNA
unique
28 days ago by
shasabhi1
• 0
0
votes
0
replies
158
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 4 days ago by
Ram
43k • written 4 days ago by
naomiboldon
• 0
0
votes
0
replies
133
views
Mitogenomes gap closure and making circular genome
gapclosure
Mitogenomes
validation
circulargenome
9 days ago by
KHURRAM SHAHZAD
• 0
0
votes
0
replies
142
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
11 days ago by
Javier
• 0
0
votes
0
replies
164
views
Homer motif analysis
Homer
10 days ago by
daffodil
▴ 10
0
votes
0
replies
106
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
5 days ago by
Javier
• 0
0
votes
0
replies
154
views
Automated internal stop codon checker
ORF
stopcodon
internal
virus
29 days ago by
Balazs Horvath
▴ 10
0
votes
0
replies
174
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 26 days ago by
Ram
43k • written 26 days ago by
bioinfo223
▴ 10
0
votes
0
replies
585
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
18 days ago by
biocellbio
• 0
0
votes
0
replies
154
views
Repeat expansion identification tools for long-read data
fragilex
repeatexpansion
long-read
fmr1
29 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
119
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
21 days ago by
ohtang7
▴ 40
0
votes
0
replies
121
views
LEfSe
LEfSe
15 days ago by
benkosta
• 0
0
votes
0
replies
232
views
create genewise sync file in popoolation
popoolation
updated 26 days ago by
GenoMax
142k • written 26 days ago by
N.Y.Wiyana-Hewage
• 0
400 results • Page
5 of 8
Recent Votes
Comment: Overlapping Ranges within Granges object
Answer: Difference between Genotype 0|1 and 1|0 in VCF file?
Answer: how to keep reads in a fasta file based on a seq id list in R?
Answer: The total expressed genes in RNA-Seq data
C: Re-arrange conditions in Seurat
Genome Visualization Tools
Answer: Genome Visualization Tools
Recent Locations •
All
London,
just now
Brazil,
1 minute ago
China,
1 minute ago
United States,
4 minutes ago
Singapore,
4 minutes ago
Sydney, Australia.,
5 minutes ago
Portugal,
6 minutes ago
Recent Awards •
All
Popular Question
to
mbrav005
• 0
Popular Question
to
Sofia
• 0
Popular Question
to
jen
▴ 10
Popular Question
to
nitinra
▴ 50
Scholar
to
Pierre Lindenbaum
161k
Scholar
to
Ram
43k
Popular Question
to
bioinfo
▴ 150
Recent Replies
Comment: Polish a large genome with Pilon
by
sansan_96
▴ 90
..........
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
you are on to something… if I use reduce to find the “overlaping regions” in a secon GRanges object, what do I do next?
Comment: Using ggplotly in R
by
jen
▴ 10
Thank you Jared for your response. I took a look at the documentation you provided and am trying my best to follow along, but can't seem to…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
by
Juke34
8.6k
Right I heard there is an issue since Perl v5.36. You may have better luck using conda. Or the best way is to use the container. Or downgra…
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
by
Mensur Dlakic
★ 27k
pLDDT scores are stored in the so-called B-factor column in PDB files. Below the `File` ribbon select `Molecule Display` and click on `b-fa…
Comment: Genome Visualization Tools
by
dlera.lozano
▴ 10
Thank you so much
Answer: Doubt about the process of annotation, detection, identification and classificat
by
Mensur Dlakic
★ 27k
Depends on the context. `TE detection` and `TE identification` could mean the same thing if they refer to presence/absence of TEs. `TE iden…
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
Ram
43k
Please accept your own answer to mark the post as solved.
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Ram
43k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Prawesh
• 0
thanks, it's working now.
Answer: Genome Visualization Tools
by
GenoMax
142k
@cmdcolin has a great list here: https://github.com/cmdcolin/awesome-genome-visualization
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Trivas
★ 1.8k
You need to have indexed your bam/sam file using `samtools index`
Answer: Using ggplotly in R
by
jared.andrews07
★ 16k
The simple answer is to plot it natively with plotly rather than use `ggplotly`. See [this stackoverflow answer](https://stackoverflow.com/…
Comment: Why does assigning genes with biomart give me different values than using a tran
by
GenoMax
142k
According to HUGO there is only one [**ZSCAN2 gene**][1] and it points to the first Ensembl gene ID (ENSG00000176371). Ensembl is annotatin…
Answer: RNAseq RNA content
by
noodle
▴ 580
There are many tools for this. I recommend [gatk (picard) CollectRnaSeqMetrics][1] or alternatively [RSeQC][2] and then run [multiqc][3…
Traffic: 2020 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