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121,937 results • Page
134 of 2439
Sort: Rank
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Votes
Replies
8
votes
16
replies
6.6k
views
9 follow
visualize CNV data based on WGS
CNV
updated 18 months ago by
clealk
▴ 80 • written 7.7 years ago by
Bogdan
★ 1.4k
1
vote
1
reply
591
views
Seeking for edgeR TMM Normalization calcul example
tmm
edgeR
deseq2
updated 18 months ago by
jared.andrews07
★ 19k • written 18 months ago by
Picasa
▴ 690
0
votes
0
replies
525
views
Tool:
MicrobiomePhylo: A Comprehensive Platform for Advanced Microbiome Amplicon Sequencing Data Analysis and Visualization
microbiome
analysis
data
16S
18 months ago by
camillatafuro
• 0
0
votes
0
replies
393
views
Tool for power calculation in GWAS for quantative trait
trait
quantative
power
calculation
GWAS
18 months ago by
chevivien
▴ 90
1
vote
1
reply
976
views
Advice for genetic diversity stats analysis with both variant and variant sites
pi
diversity
vcf
genetics
updated 18 months ago by
dthorbur
★ 3.1k • written 18 months ago by
ekirsch
• 0
0
votes
1
reply
508
views
How to find and visualize expression level of a dataset?
r
updated 18 months ago by
BioinfGuru
★ 2.1k • written 18 months ago by
uveyik
• 0
1
vote
3
replies
1.1k
views
How to validate the assembly completeness of unaligned reads ?
MaSuRCA
SPAdes
updated 18 months ago by
GenoMax
154k • written 18 months ago by
Sony
▴ 20
0
votes
3
replies
1.4k
views
Maximum returned records using epost?
E-utilities
biopython
updated 18 months ago by
GenoMax
154k • written 19 months ago by
theclubstyle
▴ 40
0
votes
1
reply
562
views
PEAR seems to have sense to me
PEAR
updated 18 months ago by
GenoMax
154k • written 18 months ago by
ManuelDB
▴ 110
0
votes
1
reply
558
views
Interprete plot of dispersion estimation by DESeq2
dispersion
DEXseq
DESeq2
updated 18 months ago by
Pierre Lindenbaum
166k • written 18 months ago by
tien
▴ 40
2
votes
3
replies
1.2k
views
Annotate genes from gtf file to vcf file
gtf
genomics
vcf
18 months ago by
QX
▴ 80
2
votes
3
replies
880
views
Read length distribution of whole genome sequnces of human
fastq
read
fastqc
18 months ago by
Yellapu
• 0
0
votes
1
reply
557
views
Adding gene to GRange objects with single base
GRanges
genomics
updated 18 months ago by
ATpoint
89k • written 18 months ago by
QX
▴ 80
2
votes
2
replies
792
views
Infering the cell composition from bulk RNA-seq data for mouse
RNA-seq
deconvolution
mouse
18 months ago by
feather-W
• 0
0
votes
2
replies
746
views
Gene set to perform GSVA
GSVA
18 months ago by
CTLong
▴ 140
6
votes
5
replies
1.2k
views
How to find gene ids for Pfam ids?
Pfam
Gene
18 months ago by
WUSCHEL
▴ 860
2
votes
4
replies
1.2k
views
Pearson correlation between Gene and clinical parameters
read-counts
Pearson-correlation
updated 18 months ago by
Shred
★ 1.6k • written 18 months ago by
Mary
• 0
0
votes
1
reply
665
views
Capped expression values in single cell RNAseq (Tabula Sapiens/scanpy/CellXGene)
scanpy
cellxgene
scRNA-seq
10x
normalisation
18 months ago by
matt.a.bennett25890
▴ 30
2
votes
1
reply
618
views
RNA-seq scaling the data for heatmap
RNA-seq
heatmap
scaling
updated 18 months ago by
matt.a.bennett25890
▴ 30 • written 18 months ago by
maplewj
▴ 20
3
votes
11
replies
1.6k
views
bedToBigBed error, what am I doing wrong?
Homer
software-error
UCSC
updated 18 months ago by
Pierre Lindenbaum
166k • written 18 months ago by
Ronin
▴ 10
3
votes
2
replies
1.8k
views
R: How to customize the legend order for a 3D scatter plot in plotly?
R
r
plotly
18 months ago by
SIV0625TriX
▴ 30
7
votes
3
replies
3.7k
views
Single cluster spanning in different locations in UMAP in scRNAseq data
UMAP
scRNAseq
18 months ago by
sarahmanderni
▴ 130
0
votes
4
replies
1.1k
views
Biostrings extract read
R
fastq
Biostrings
18 months ago by
marco.barr
▴ 180
1
vote
2
replies
870
views
Detecting viruses in human rna seq data
RNA-Seq
Viruses
updated 18 months ago by
GenoMax
154k • written 18 months ago by
biochugs
• 0
0
votes
0
replies
502
views
Change orig.ident column in seurat meta.data to match cell barcode sample prefixes
seurat
18 months ago by
bgbs
• 0
1
vote
2
replies
859
views
Length by gene from salmon
salmon
RNA-seq
18 months ago by
marco.barr
▴ 180
5
votes
4
replies
1.9k
views
change order of violin plots in ggplot2
R
ggplot2
violin-plots
updated 18 months ago by
Ram
45k • written 18 months ago by
Matteo Ungaro
▴ 130
0
votes
0
replies
394
views
Motif analysis by HOMER
Homer
18 months ago by
daffodil
▴ 10
1
vote
2
replies
1.4k
views
Applicability of the SoupX ambient mRNA decontamination technique to fixed and/or multiplexed scRNAseq experiments
SoupX
scRNA-seq
18 months ago by
e.r.zakiev
▴ 260
0
votes
5
replies
1.7k
views
Error when trying to install R package 'scater'
scater
scRNA-Seq
updated 18 months ago by
Ram
45k • written 18 months ago by
Nitin
• 0
1
vote
4
replies
1.6k
views
Long branch lengths, low bootstrap values and misalignments
mafft
muscle
iqtree
18 months ago by
samyu.senthil
▴ 10
5
votes
5
replies
1.4k
views
Including reference genome in SNP-based phylogeny
phylogeny
VCF
WGS
18 months ago by
maxrwjones
▴ 60
2
votes
5
replies
1.0k
views
How to add FORMAT/TAG = "." to all samples in a vcf file via bcftools?
vcf
bcftools
updated 18 months ago by
Pierre Lindenbaum
166k • written 18 months ago by
Марта
• 0
1
vote
1
reply
653
views
adding new assemblies to previously built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
updated 18 months ago by
lcj34
▴ 420 • written 18 months ago by
b.contreras.moreira
▴ 490
0
votes
2
replies
971
views
Ribo and RNA seq analysis
RNA-seq
genomics
Ribo-seq
updated 18 months ago by
Jack Tierney
▴ 450 • written 19 months ago by
Manu Ayllon
• 0
0
votes
0
replies
444
views
DADA2 truncLen value
metabarcoding
phyloseq
DADA2
illumina
18 months ago by
Bioinfo
▴ 20
0
votes
3
replies
817
views
Resources regarding Proteomics (In-Silico)
molecular-simulation
docking
protein
proteomics
updated 18 months ago by
Ram
45k • written 18 months ago by
Saurabh
• 0
0
votes
5
replies
1.8k
views
Deeptools scale issue for plotHeatmap
deeptools
computeMatrix
plotHeatmap
18 months ago by
Learner
• 0
4
votes
1
reply
1.3k
views
why there is an asterisk symbol at the end of each proteins sequences of fasta files in the Braker3 output?
gtf
breaker3
protein-seq
18 months ago by
mathavanbioinfo
▴ 80
1
vote
5
replies
1.4k
views
Haddock 2.4
Protein
Docking
updated 18 months ago by
dthorbur
★ 3.1k • written 18 months ago by
Preeti
• 0
0
votes
2
replies
2.1k
views
Beagle Phasing and Imputation
imputation
phasing
beagle
18 months ago by
Duarte Molha
▴ 240
1
vote
0
replies
392
views
ENVO Ontology to Annotate Plain Text
natural
language
NL
ontology
envo
18 months ago by
marie.harmel
▴ 10
2
votes
4
replies
6.1k
views
Subsetting Seurat object based on list of cell barcodes
seurat
updated 18 months ago by
Ming Tommy Tang
★ 4.7k • written 18 months ago by
bgbs
• 0
34
votes
16
replies
24k
views
14 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 18 months ago by
aUser
▴ 80 • written 9.0 years ago by
martinguerrerog89
▴ 310
0
votes
1
reply
551
views
Issues With Cram -> Fastq from GTEx v8 WGS
fastq
GTEx
cram
updated 18 months ago by
Pierre Lindenbaum
166k • written 18 months ago by
Vullnet
• 0
0
votes
2
replies
702
views
DEG (Differential expression gene) analysis
DEG
R
updated 18 months ago by
dsull
★ 7.7k • written 18 months ago by
sooni
▴ 20
0
votes
2
replies
777
views
Biobambam vs Picard in RNA Sequencing Analysis for BAM to FASTQ
RNA-seq
Biobambam
Picard
18 months ago by
kcarey
• 0
0
votes
0
replies
450
views
News:
Online course: Adaptation Genomics
StructuralVariants
Selection
AdaptationGenomics
PopulationStructure
18 months ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
391
views
News:
Online course: Analysis of Prokaryotic Pangenomes
BacterialGenomics
Pangenomics
18 months ago by
Physalia-courses
★ 2.6k
1
vote
2
replies
1.0k
views
Is it better to pool samples prior to running deseq2, or should the algorithm be run separately for every pool?
deseq2
RNA-seq
18 months ago by
Shelby
• 0
121,937 results • Page
134 of 2439
Recent Votes
A: How to normalize my rna seq data?
Answer: Linear regression vs DESeq2 models for DEG analysis
Answer: Linear regression vs DESeq2 models for DEG analysis
Answer: Linear regression vs DESeq2 models for DEG analysis
Answer: Linear regression vs DESeq2 models for DEG analysis
Answer: Linear regression vs DESeq2 models for DEG analysis
Answer: Linear regression vs DESeq2 models for DEG analysis
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nuorain
▴ 40
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charms.charms
• 0
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Recent Replies
Comment: Linear regression vs DESeq2 models for DEG analysis
by
ATpoint
89k
+1 Our answer should be the top-voted answer in this thread https://www.biostars.org/p/284775/ as it actually addresses conceptual differ…
Comment: Linear regression vs DESeq2 models for DEG analysis
by
swbarnes2
15k
It is not clear to me that you can meaningfully correct for 5 different batches with two samples a piece.
Comment: Does this adapter content from fastqc to warrant trimming prior to alignment?
by
GenoMax
154k
> I am not sure if there would be primer dimer sequences I should have said adapter dimers above. Correction made.
Comment: Help understanding this per base sequence content failure fastqc plot
by
lieven.sterck
15k
that 151st base added is a base to ignore (it's a kind of random addition) ... if I recall correctly it's a consequence of the technology. …
Comment: Linear regression vs DESeq2 models for DEG analysis
by
FioG
• 0
@swbarnes2 Thank you for your response! I am new to RNA seq analysis and was originally recommended to use the LM method following cqn and …
Comment: Does this adapter content from fastqc to warrant trimming prior to alignment?
by
curious
▴ 890
Thank you, the adapter sequences are specified as CTGTCTCTTATACACATCT+ATGTGTATAAGAGACA is the SampleSheet.csv file from the sequencing run.…
Comment: how to explain the sample size discrepancy in UCSC Xena
by
nuorain
▴ 40
Thank you very much.
Answer: how to explain the sample size discrepancy in UCSC Xena
by
i.sudbery
22k
Because there wasn't RNA-seq analysis performed for every sample in TCGA?
Answer: Linear regression vs DESeq2 models for DEG analysis
by
i.sudbery
22k
There are two main problems with using linear models for read-count based analyses. Firstly, linear models assume a normal distribution…
Comment: real time PCR data analysis
by
ATpoint
89k
I cannot guide on GraphPad. It's commercial software so better contact their support.
Answer: Linear regression vs DESeq2 models for DEG analysis
by
swbarnes2
15k
DE genes in bulk RNASeq is what DESeq2 was made for, so why wouldn't you use it? RPKM is not an appropriate normalization method here. M…
Comment: What happened to biomart.org
by
Jeremy Leipzig
23k
same with geuvadis.org
Comment: real time PCR data analysis
by
Gordon Smyth
★ 8.3k
Are you doing qPCR for one gene or for several genes?
Comment: protein interaction prediction
by
Fatemeh
▴ 50
Thanks very much for your help. I need to try it.
Comment: real time PCR data analysis
by
Fatemeh
▴ 50
Thanks a lot for the link. The problem is that with this repeated measures, if you put the data from different donors in different rows, fo…
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