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400 results • Page
4 of 8
Sort: Votes
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Views
Votes
Replies
0
votes
0
replies
199
views
Chemical structure validation
structure
cap
validation
metabolite
25 days ago by
Rodolfo Adrián
• 0
0
votes
2
replies
216
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 4 days ago by
Ram
43k • written 5 days ago by
sainavyav22
• 0
0
votes
0
replies
63
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
17 hours ago by
Spring
• 0
0
votes
2
replies
291
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 2 days ago by
Zhenyu Zhang
★ 1.2k • written 11 days ago by
yahn
• 0
0
votes
0
replies
115
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
22 days ago by
Enrique
• 0
0
votes
0
replies
157
views
Filter low express genes in microarray data
microarray
17 days ago by
Chris
▴ 280
0
votes
1
reply
131
views
How to process Bulk WES data?
WES
WGS
updated 1 day ago by
GenoMax
142k • written 1 day ago by
wyuan37
• 0
0
votes
0
replies
2.0k
views
NOISeq Batch Correction to RNA-seq data
Batch-effect
RNA-Seq
ARSyNseq
limma
NOISeq
updated 26 days ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
0
votes
1
reply
183
views
unable to get feature count results
featureCounts
updated 14 days ago by
Ram
43k • written 14 days ago by
Ravita
• 0
0
votes
0
replies
51
views
Retrieving ceRNA data from the starBase or ENCORI Web API
ceRNA
ENCORI
WebAPI
microRNA
starBase
updated 10 hours ago by
GenoMax
142k • written 10 hours ago by
Bhavya
• 0
0
votes
3
replies
302
views
Snakemake wrapper issue
fastqc
snakemake
updated 18 hours ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
87
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
20 hours ago by
Holly
• 0
0
votes
1
reply
142
views
consensus sequence calling
consensus
updated 1 day ago by
bk11
★ 2.4k • written 1 day ago by
Ghada
• 0
0
votes
0
replies
2.7k
views
Comparing lists generated by Counter() and .most_common() for AA seqs
python
amino-acid
updated 27 days ago by
Ram
43k • written 9.9 years ago by
st.ph.n
★ 2.7k
0
votes
1
reply
305
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 27 days ago by
GenoMax
142k • written 27 days ago by
ycts
• 0
0
votes
0
replies
231
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 26 days ago by
Ram
43k • written 26 days ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
177
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
5 days ago by
Winter
• 0
0
votes
0
replies
103
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
eigencorplot
PCAtools
deseq2
pca
2 days ago by
BioinfGuru
★ 1.7k
0
votes
0
replies
1.3k
views
which value from ruvadj in missMethyl can present methylation status
R
RUV
methylation
missmethyl
batch-effect
updated 28 days ago by
Ram
43k • written 6.0 years ago by
RC
▴ 20
0
votes
0
replies
109
views
Cellphonedb results
cpdb
visulization
cellphonedb
8 days ago by
piotto
▴ 20
0
votes
0
replies
157
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
14 days ago by
O.rka
▴ 720
0
votes
2
replies
307
views
Annovar using R package
Annovar
gnomAD
R
19 days ago by
DKA
▴ 40
0
votes
2
replies
219
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
1 day ago by
analyst
▴ 50
0
votes
2
replies
276
views
How are score_weights calculated in this code?
single-cell
3 days ago by
carolofharvest
▴ 40
0
votes
1
reply
155
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 6 days ago by
Bastien Hervé
5.3k • written 6 days ago by
sooni
▴ 20
0
votes
2
replies
221
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
12 days ago by
dtnondorf
• 0
0
votes
0
replies
1.8k
views
Accounting for hidden batch effects in differential expression analysis with DEXseq and Slueth
Batch-effect
RNA-Seq
Differential-Expression
updated 27 days ago by
Ram
43k • written 7.2 years ago by
vakul.mohanty
▴ 270
0
votes
1
reply
555
views
HOMER on AWS
HOMER
updated 11 days ago by
clairechung112
• 0 • written 2.2 years ago by
Bogdan
★ 1.4k
0
votes
5
replies
452
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 17 days ago by
Istvan Albert
100k • written 20 days ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
900
views
Advice on group specific condition effect and model matrix in deseq2
deseq2
batch-effect
updated 29 days ago by
Ram
43k • written 4.1 years ago by
Mozart
▴ 330
0
votes
1
reply
168
views
tbtool
tbtool
updated 22 days ago by
Ram
43k • written 22 days ago by
Raman
• 0
0
votes
0
replies
171
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
19 days ago by
Aspire
▴ 330
0
votes
0
replies
196
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
26 days ago by
P.
• 0
0
votes
0
replies
1.9k
views
How to get Gene Co-expression Network from RNA seq data using cor() function?
RNA-Seq
gene-expression-matrix
correlation
R
updated 27 days ago by
Ram
43k • written 6.3 years ago by
aiswaryabioinfo
▴ 30
0
votes
0
replies
150
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
4 days ago by
Samantha
• 0
0
votes
0
replies
211
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
27 days ago by
synat.keam
▴ 100
0
votes
0
replies
149
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
5 days ago by
Aytaç
• 0
0
votes
0
replies
602
views
Differential accessibility using DiffBinf
diffbind
15 days ago by
Shloka
• 0
0
votes
0
replies
137
views
Add geno header to VariantAnnotation objects
nichenet
scRNA-seq
28 days ago by
QX
• 0
0
votes
1
reply
224
views
How to get the reference panel sites for TOPMed hg37 and 38
Imputation
updated 29 days ago by
bk11
★ 2.4k • written 29 days ago by
sinhas
• 0
0
votes
5
replies
6.0k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 24 days ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 30
0
votes
0
replies
1.5k
views
minifi for RRBS
rrbs
batch-effect
methylation
updated 27 days ago by
Ram
43k • written 7.2 years ago by
German.M.Demidov
★ 2.9k
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
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 26 days ago by
Ram
43k • written 7.1 years ago by
endikavarela
• 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
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
154
views
Automated internal stop codon checker
ORF
stopcodon
internal
virus
29 days ago by
Balazs Horvath
▴ 10
0
votes
4
replies
218
views
Galaxy StringTie error
stringtie
galaxy
13 hours ago by
trkfs
• 0
400 results • Page
4 of 8
Recent Votes
C: Re-arrange conditions in Seurat
Genome Visualization Tools
Comment: Genome Visualization Tools
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
A: Best de novo assembler for insect genome ?
Comment: sci-RNA-seq
The Biostar Herald for Monday, May 13, 2024
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jen
▴ 10
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nitinra
▴ 50
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Recent Replies
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.
Comment: 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…
Comment: Where to get the following bed file?
by
wyuan37
• 0
Hi, I emailed them and did get the bed file! Thank you so much.
Comment: Where to get the following bed file?
by
wyuan37
• 0
Thanks! Super helpful.
Answer: Post-imputation QC for input into GWAS analyses
by
LauferVA
4.2k
1. Imputation algorithms will output log files indicating, among other things, accuracy of imputation. We can't comment on specifics as we …
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data
by
GenoMax
142k
You can simply ignore read 2. It is not adding any information since your small RNA's are going to be small and were completely sequenced b…
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
does this work with a single .bed file?
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