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121,975 results • Page
240 of 2440
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Votes
Replies
8
votes
5
replies
1.8k
views
Should primary tumor RNA-Seq match their derived cell lines and PDXs? And which dimensionality reduction method should I use?
PDX
dimensionality-reduction
RNA-Seq
PCA
2.2 years ago by
sarahgzb
▴ 40
0
votes
2
replies
1.3k
views
GSEA vs Functional Annotation
Set
Analysis
Gene
Enrichment
updated 2.3 years ago by
LauferVA
4.8k • written 2.3 years ago by
turcoa1
• 0
0
votes
1
reply
1.0k
views
BRAKER for large genome?
samtools
BRAKER
CSI
annotation
BAM
updated 2.3 years ago by
Buffo
★ 2.4k • written 2.3 years ago by
Dave
• 0
2
votes
5
replies
1.5k
views
complex heatmap
rna-seq
complexheatmap
updated 2.3 years ago by
Ming Tommy Tang
★ 4.7k • written 2.3 years ago by
biology_inform
▴ 60
1
vote
3
replies
2.0k
views
Rarefaction curve of microbiome study
Rarefaction
updated 2.3 years ago by
Asaf
10k • written 2.3 years ago by
aea55647
• 0
0
votes
0
replies
1.1k
views
Tutorial:
How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq
rstats
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
Ming Tommy Tang
★ 4.7k
1
vote
0
replies
1.3k
views
How to get/write a .gmt file corresponding to the databases queried by the gseGO() function of clusterProfiler ?
GO.db
org.Hs.eg.db
GSEA
clusterProfiler
2.3 years ago by
am835821
▴ 10
0
votes
6
replies
1.8k
views
Large-scale bulk RNAseq Experiment with abnormal MA-plots for apoptotic conditions
MA-plot
DESeq2
Smartseq2
2.3 years ago by
Nico
• 0
4
votes
4
replies
2.8k
views
Visualize methylation status in Pacbio Hifi read
Pacbio
methylation
2.3 years ago by
Cathy
▴ 10
0
votes
2
replies
887
views
Multiple Tumor Count Files from a single Patient. How to merge or select?
Cancer
GDC
RNA-SEQ
2.0 years ago by
Rishav
• 0
0
votes
1
reply
1.1k
views
How to extract list of top 10 markers from each cluster?
R
Seurat
single-cell
cluster
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
Bioinfo
▴ 30
0
votes
6
replies
2.0k
views
creating conda environment from snakemake rule
snakemake
conda
2.3 years ago by
Jordi
▴ 60
2
votes
12
replies
3.0k
views
gatk Funcotator
vcf
Funcotator
gatk
2.3 years ago by
Saurabh
• 0
0
votes
2
replies
1.1k
views
Variant format conversion to genome coordinates
dbsnp
GeneSymbol
HGVS
Variants
RefSeq
2.3 years ago by
krishnajandhyalaa
• 0
3
votes
12
replies
2.5k
views
Check if blastn gene matches are of entire genes or of parts of genes
blastx
blastn
bacteria
2.3 years ago by
langziv
▴ 70
0
votes
1
reply
2.1k
views
clusterProfiler
clusterProfiler
updated 2.3 years ago by
LauferVA
4.8k • written 2.3 years ago by
CaroH
▴ 10
0
votes
1
reply
802
views
including incomplete data set in the PCA & gene expression analysis
RNA-seq
updated 2.3 years ago by
LauferVA
4.8k • written 2.3 years ago by
Sara
▴ 280
0
votes
1
reply
1.1k
views
3' Single Cell RNA Seq Reads mapping to promoter region of gene
promoter
single-cell
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
rekharichardson
• 0
0
votes
1
reply
947
views
Should genotype PCA in eQTL analysis be performed using all SNPs? or can be with a subset of SNPs?
genotype
eQTL
SNP
PCA
updated 2.3 years ago by
LauferVA
4.8k • written 2.3 years ago by
maximal_life
▴ 20
0
votes
9
replies
2.3k
views
gene id
gene-id
NCBI
updated 2.3 years ago by
GenoMax
154k • written 2.3 years ago by
safeassli
▴ 10
2
votes
1
reply
777
views
How to normalize intron counts?
DESeq
limma
RNA-SEQ
updated 2.3 years ago by
Asaf
10k • written 2.3 years ago by
PK
▴ 130
1
vote
1
reply
686
views
Does latent classification analysis need a separate verification bias removal? how to perform that?
latent-classification
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
sukeshinik5
▴ 50
1
vote
3
replies
1.4k
views
VEP: Generation of polyphen2 & SFT scores for structural variants.
Structural-Variant
VEP
Polyphen2
updated 2.3 years ago by
LauferVA
4.8k • written 2.3 years ago by
The_PyPanda
▴ 10
0
votes
0
replies
563
views
News:
Course - Data Manipulation and Visualization in Python
Data-Manipulation
Data-Visualisation
Python
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
421
views
appropriate parameter of software GONE
linkage-disequilibrium
GONE
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
TN
• 0
0
votes
1
reply
1.5k
views
Annovar Error
annovar
2.3 years ago by
ttom
▴ 230
0
votes
1
reply
1.3k
views
Putting Multiple ANOVA P-Values on Violin Plot
violin
R
ANOVA
updated 2.3 years ago by
Asaf
10k • written 2.3 years ago by
cthangav
▴ 110
0
votes
0
replies
541
views
ComBat returns negative expression value
SVA
batch
ComBat
R
2.3 years ago by
Grace
• 0
0
votes
2
replies
1.7k
views
Error: free(): invalid next size (fast) and Aborted (core dumped) while using R in Linux server
WGBS
R
MethylKit
2.3 years ago by
Sowmya Pulapet
▴ 70
3
votes
4
replies
1.3k
views
IsoformSwitchAnalyzeR Error in reading GTF file
R
IsoformSwitchAnalyzeR
2.3 years ago by
VenGeno
▴ 100
0
votes
0
replies
723
views
Does Minknow in nanopore sequencing trim low qscore bases?
filtering
nanopore
qc
minknow
ont
2.3 years ago by
grkorompis
• 0
1
vote
1
reply
817
views
How to remove batch effect from TCGA RNA-seq data?
BATCH-EFFECT
WGCNA
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
Khas-erdene
• 0
1
vote
6
replies
2.4k
views
warning[vg::Watchdog]
vg
Watchdog
giraffe
updated 2.3 years ago by
colindaven
8.0k • written 2.3 years ago by
hxt
• 0
2
votes
2
replies
2.8k
views
Seurat: Log fold change and p value when control expression is 0
RNA-seq
DGE
updated 2.3 years ago by
LauferVA
4.8k • written 2.3 years ago by
psm
▴ 170
0
votes
0
replies
548
views
Aligning/comparing different versions of the human genome and their GTFs
Alignment
Human
Genome
2.3 years ago by
murphytho1401
• 0
4
votes
2
replies
1.2k
views
Good tool/best practice for filtering out homopolymeric reads?
quality-control
metagenomics
data-cleaning
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
Sean
▴ 10
0
votes
0
replies
611
views
How to integrate cross species from Microarray and RNAseq?
Microarray
RNA-seq
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
vinothkumarvtech2023
• 0
0
votes
0
replies
454
views
how to calculate predicted expression using weights from model file
predicted-expression
R
predixcan
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
rheab1230
▴ 150
2
votes
2
replies
1.1k
views
Batch correction score and bio conservation score how to get those?
Batch-correction
bio-conservation
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
Andy
▴ 120
1
vote
2
replies
1.1k
views
Jensen-Shannon Divergence (Capra and Singh, 2007) scored with substitution matrix for conservation score
multiple-sequence-alignment
conservation
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
Jonathan Lefebre
▴ 70
0
votes
1
reply
840
views
Tools for getting significant interactions in the HiC-data?
3div
hic
updated 2.3 years ago by
Buffo
★ 2.4k • written 2.3 years ago by
NikhilP
▴ 20
4
votes
6
replies
2.0k
views
Very different QUAL scores on VCFs of same sample using different methods
deepvariant
clara-parabricks
haplotypecaller
vcf
2.3 years ago by
Victor
▴ 20
1
vote
2
replies
1.6k
views
Guide to Installing OpenJDK Version 1.8.0_352 on Ubuntu for Picard Tool Compatibility
picard
jdk8
java
updated 2.3 years ago by
Mensur Dlakic
★ 30k • written 2.3 years ago by
Nour-eddine
▴ 70
3
votes
4
replies
6.5k
views
How to get the corresponding PMCID from PMID with python?
Pubmed
PMCID
PMID
updated 2.3 years ago by
Wasim Aftab
• 0 • written 7.3 years ago by
flaviellebm
• 0
3
votes
8
replies
1.7k
views
Can these RNAseq runs be combined?
transcriptomics
replicates
RNAseq
updated 2.3 years ago by
GenoMax
154k • written 2.3 years ago by
mdrnao
• 0
0
votes
0
replies
577
views
Shiu pipeline for pseudogene prediction from genome
prediction
intronlength
pseudogene
repeatmasking
pseudoexon
2.3 years ago by
subashini.fbtpb106
▴ 20
2
votes
3
replies
5.0k
views
Merge really large amount of Seurat objects
Seurat
2.3 years ago by
Andy
▴ 120
1
vote
4
replies
1.8k
views
Annotation of spatial data
cell-annotation
visium
2.2 years ago by
abiuma
▴ 30
0
votes
0
replies
505
views
Filtering of mCs before downstream DMR analysis
WGBS
DMR
metilene
Bismark
2.3 years ago by
poa.alpina
• 0
1
vote
8
replies
2.5k
views
Why did GENCODE change the main annotation file from Comprehensive to Basic
GENCODE
2.3 years ago by
gernophil
▴ 130
121,975 results • Page
240 of 2440
Recent Votes
Answer: Quantification using salmon in alignment-based mode after minimap2 run
Answer: Quantification using salmon in alignment-based mode after minimap2 run
Answer: vcf to bam
Tumor grade from miRNA data set from TCGA database
Answer: Nextflow: How to format input tuple for STAR_ALIGN process with STAR index direc
Answer: Nextflow: How to format input tuple for STAR_ALIGN process with STAR index direc
Answer: GUI commercial software for 10x single cell gene expression analysis
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Comment: tximport error (medianLengthOverIsoform)
by
LGG
• 0
I believe using `ignoreTxVersion = TRUE` is supposed to take care of that
Answer: Which aligner is more suitable for ONT R10.4.1 Dorado-corrected reads: minimap2
by
tungsega
▴ 10
Just a very brief summary of the results using the latest versions of minimap2 and winnowmap (by `samtools stats`). It seems that winnowma…
Comment: Quantification using salmon in alignment-based mode after minimap2 run
by
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★ 1.9k
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Comment: Quantification using salmon in alignment-based mode after minimap2 run
by
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★ 1.9k
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I needed to be aware of queue channels which you can read about here: https://training.nextflow.io/2.0/basic_training/channels/#queue-c…
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I am looking back now, and it appears that the files processed after kmer correction (rcorrector) seem to match up, except the first sample…
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Cloud solution: Partek Flow (going to be called Illumina Multiomics at some point soon, Partek was purchased by Illumina a couple of years …
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People publish predictive papers all the time that have zero experimental support. There are different degrees of "lacking experimental val…
Comment: how to respond that my research does not have experimental validation
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89k
You should give the reviewer something. An independent way of in silico validation, other supporting analysis. Just "no" might lead to reje…
Answer: Which aligner is more suitable for ONT R10.4.1 Dorado-corrected reads: minimap2
by
okiedokie1208
▴ 40
I believe ONT recommends Minimap2. This is also the default tools in their EPI2ME workflow.
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Yes, and if you are going to mention that experimental validation is not possible or outside the scope of your paper, kindly remind the rev…
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Is it possible that mismatched R1/R2 files were used in one of the steps? If you are sure that has not happened then you could try to see…
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154k
In case you were not aware ONT also provides a transcriptome workflow for long reads: https://github.com/epi2me-labs/wf-transcriptomes
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89k
Either do experimental validation, or say that not possible due to lack of collaboration, infrastructure, lab background. If they reject, s…
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7.1k
As @atpoint suggests, you must align against the transcriptome. Also, the other relevant flags should be set (i.e. `--secondary=no` will di…
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