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1,000 results • Page
4 of 20
Sort: Rank
Rank
Views
Votes
Replies
2
votes
3
replies
331
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 15 days ago by
dthorbur
★ 2.0k • written 15 days ago by
Vijith
▴ 30
0
votes
0
replies
162
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
15 days ago by
Jeyong
• 0
0
votes
0
replies
152
views
Empty table plot using plotGseaTable()
FGSEA
15 days ago by
Chris
▴ 280
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 16 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
242
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
16 days ago by
dtnondorf
• 0
3
votes
8
replies
621
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
12 days ago by
Qroid
▴ 40
0
votes
1
reply
182
views
Provean help
variant
Provean
updated 16 days ago by
Mensur Dlakic
★ 27k • written 16 days ago by
Arun Sai Kumar
• 0
0
votes
0
replies
114
views
Use of annotation of integrated Seurat object in single sample
Seurat
16 days ago by
Bine
▴ 60
0
votes
1
reply
264
views
Subsetting and merging back Seurat Object brings different results
Seurat
16 days ago by
Bine
▴ 60
1
vote
1
reply
169
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 16 days ago by
Ram
43k • written 16 days ago by
marco.barr
▴ 130
0
votes
0
replies
110
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
16 days ago by
Vijith
▴ 30
0
votes
0
replies
117
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
16 days ago by
James
▴ 10
0
votes
1
reply
611
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 17 days ago by
mdav
• 0 • written 19 months ago by
Zoe
• 0
1
vote
3
replies
295
views
Odd alignment question/finding
Alignment
updated 15 days ago by
barslmn
★ 2.2k • written 17 days ago by
poordumbsillyidiot
• 0
0
votes
1
reply
237
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 17 days ago by
GenoMax
142k • written 17 days ago by
mgranada3
▴ 30
0
votes
0
replies
136
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 17 days ago by
Ram
43k • written 17 days ago by
Oscar
▴ 10
0
votes
1
reply
180
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 17 days ago by
Ram
43k • written 17 days ago by
ernestine.kubi
• 0
0
votes
0
replies
122
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
17 days ago by
VITALA
• 0
1
vote
2
replies
294
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
16 days ago by
rianna.collins
• 0
0
votes
1
reply
205
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 17 days ago by
i.sudbery
19k • written 18 days ago by
Edmond
• 0
0
votes
0
replies
163
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
18 days ago by
O.rka
▴ 720
0
votes
1
reply
704
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 17 days ago by
Ram
43k • written 18 days ago by
Dr Huma Naz
• 0
0
votes
5
replies
433
views
Telescope issue
Telescope
RNA-seq
updated 17 days ago by
GenoMax
142k • written 18 days ago by
eleven11
• 0
1
vote
1
reply
257
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 18 days ago by
Ram
43k • written 18 days ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
324
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
17 days ago by
Nafi
• 0
1
vote
3
replies
330
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 18 days ago by
GenoMax
142k • written 18 days ago by
jeffrey.maurer.informatics
• 0
0
votes
2
replies
259
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
11 days ago by
Ahiad Chen Zion
• 0
0
votes
0
replies
140
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 18 days ago by
Ram
43k • written 18 days ago by
Alexandros
• 0
0
votes
1
reply
192
views
unable to get feature count results
featureCounts
updated 18 days ago by
Ram
43k • written 18 days ago by
Ravita
• 0
0
votes
3
replies
323
views
KEGG Pathways
r
RNA-seq
updated 18 days ago by
Ram
43k • written 18 days ago by
Sudip
• 0
0
votes
0
replies
152
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
18 days ago by
Bine
▴ 60
1
vote
2
replies
257
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 18 days ago by
Ram
43k • written 18 days ago by
Ravita
• 0
3
votes
3
replies
274
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 5 days ago by
Ram
43k • written 18 days ago by
Adyasha
• 0
0
votes
0
replies
123
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
18 days ago by
fanglujing
▴ 60
0
votes
0
replies
149
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
19 days ago by
Jacob
• 0
0
votes
1
reply
203
views
Differential Accessibility
DiffBind
updated 19 days ago by
Ram
43k • written 19 days ago by
Shloka
• 0
0
votes
3
replies
324
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 18 days ago by
GenoMax
142k • written 19 days ago by
kim
• 0
3
votes
7
replies
421
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
19 days ago by
salias
• 0
0
votes
0
replies
141
views
Using limma in methylation EM-seq?
EM-seq
methylation
19 days ago by
Lluís R.
★ 1.2k
0
votes
0
replies
138
views
Synteny analysis
bacterial
synteny
genome
updated 19 days ago by
GenoMax
142k • written 19 days ago by
Namil
• 0
0
votes
4
replies
309
views
Genbank File Format
gbkformat
18 days ago by
alenew.am
• 0
0
votes
0
replies
272
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
19 days ago by
SSSJec
• 0
0
votes
3
replies
262
views
Software to separate reads from different individuals
software
development
nanopore
updated 19 days ago by
GenoMax
142k • written 19 days ago by
njornet
▴ 20
0
votes
2
replies
370
views
How to update R on ubuntu
installation
update
R
apt-get
19 days ago by
Bosberg
▴ 50
0
votes
0
replies
128
views
LEfSe
LEfSe
19 days ago by
benkosta
• 0
0
votes
0
replies
104
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
19 days ago by
Sara
▴ 30
0
votes
2
replies
199
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
19 days ago by
Lluís R.
★ 1.2k
0
votes
0
replies
124
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 5 days ago by
Ram
43k • written 19 days ago by
atharvakarkare14
▴ 40
0
votes
2
replies
248
views
What should I consider as FASTA for dataset?
PDB
FASTA
19 days ago by
Nafi
• 0
0
votes
0
replies
609
views
Differential accessibility using DiffBinf
diffbind
19 days ago by
Shloka
• 0
1,000 results • Page
4 of 20
Recent Votes
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
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synat.keam
▴ 100
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jv
★ 1.8k
Popular Question
to
syedahamdani94
• 0
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Recent Replies
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
by
anton.i.petrov
• 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
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