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900 results • Page
6 of 18
Sort: Views
Rank
Views
Votes
Replies
0
votes
1
reply
842
views
How to compare differentially expressed genes among different affymatrix dataset
microarray
batch-effect
R
updated 28 days ago by
Ram
43k • written 4.8 years ago by
Calangoa
▴ 30
2
votes
3
replies
838
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 11 days ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
0
votes
1
reply
834
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR
Batch-effect
RNA-Seq
updated 27 days ago by
Ram
43k • written 3.7 years ago by
jordan15
• 0
3
votes
2
replies
831
views
Retrieve initial query in getBM()
getBM
biomaRt
R
gene
updated 28 days ago by
Ram
43k • written 3.2 years ago by
helia.ziaei
• 0
0
votes
2
replies
829
views
Is it correct to merge two raw CEL datasets and then perform quality control, background correction, and normalization on it?
R
microarray
affymetrix
batch-effect
quality-control
updated 29 days ago by
Ram
43k • written 2.9 years ago by
Sib
▴ 60
1
vote
2
replies
828
views
What type of normalization does removeBatchEffect function require as the input?
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 29 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
1
vote
5
replies
804
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 26 days ago by
BioinfGuru
★ 1.7k • written 27 days ago by
rrehimi
• 0
4
votes
6
replies
799
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 18 days ago by
dsull
★ 6.0k • written 22 days ago by
qudrat.nii
▴ 10
0
votes
1
reply
797
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 13 days ago by
Ram
43k • written 2.7 years ago by
carov
• 0
2
votes
5
replies
783
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 25 days ago by
Jesse
▴ 770 • written 26 days ago by
Ann
★ 2.4k
0
votes
1
reply
778
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 17 days ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
1
vote
4
replies
766
views
What happened to Tombo Re-squiggle
Tombo
resquiggle
ONT
updated 27 days ago by
Ram
43k • written 3 months ago by
turcoa1
• 0
0
votes
3
replies
763
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 16 days ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
4
votes
8
replies
760
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 19 days ago by
Alex Reynolds
35k • written 19 days ago by
J
▴ 10
5
votes
3
replies
757
views
Illumina reads preprocessing best practice for snp calling applications
Illumina
snp
updated 26 days ago by
Enrique
• 0 • written 10 months ago by
Denis
▴ 310
3
votes
3
replies
749
views
KissDE and batch effect
kissDE
kissplice
23 days ago by
david.b.rombaut
▴ 10
3
votes
6
replies
748
views
Ciriquant not configuring hisat2 indexed files
ciriquant
23 days ago by
Atul K.
• 0
8
votes
8
replies
748
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 20 days ago by
swbarnes2
14k • written 21 days ago by
Aaliya
▴ 10
0
votes
2
replies
744
views
homer not configured properly
Homer
makeTagDirectory
updated 13 days ago by
clairechung112
• 0 • written 24 months ago by
amahdi779
• 0
3
votes
4
replies
743
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
23 days ago by
rahu
• 0
10
votes
14
replies
742
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 8 days ago by
GenoMax
142k • written 14 days ago by
nicole.kavanagh
• 0
1
vote
5
replies
742
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
0
votes
0
replies
741
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq
scRNA-Seq
batch-effect
updated 27 days ago by
Ram
43k • written 3.5 years ago by
hkarakurt
▴ 180
0
votes
0
replies
739
views
"No group or design set" with deAna() function in EnrichmentBrowser package
RNA-Seq
R
EnrichmentBrowser
updated 28 days ago by
Ram
43k • written 4.1 years ago by
yxswhx
• 0
1
vote
6
replies
720
views
anRichment is missing
WGCNA
anRichment
updated 9 days ago by
GenoMax
142k • written 6 months ago by
michael.flower.14
▴ 180
2
votes
4
replies
719
views
Count all variants from vcf file
variants
vcf
Count
updated 8 days ago by
Pierre Lindenbaum
161k • written 20 months ago by
t.ali
• 0
5
votes
4
replies
716
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq
EdgeR
DEGs
DESeq2
27 days ago by
BioinfGuru
★ 1.7k
5
votes
4
replies
711
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
21 days ago by
kirillkirilenko
▴ 40
0
votes
11
replies
707
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
20 days ago by
atowns21
• 0
0
votes
1
reply
699
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 15 days ago by
Dr Huma Naz
• 0
0
votes
3
replies
690
views
Pluritest for pluripotency broken
pluripotent
pluritest
cells
stem
updated 6 days ago by
DGTool
• 0 • written 21 months ago by
yassine
• 0
3
votes
10
replies
690
views
Piping samtools to R
R
NGS
bash
samtools
29 days ago by
noodle
▴ 580
1
vote
0
replies
681
views
Conditions for valid batch effect correction
r
batch-effect
updated 29 days ago by
Ram
43k • written 5.2 years ago by
Sebastian Hesse
▴ 340
2
votes
9
replies
681
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 19 hours ago by
Pierre Lindenbaum
161k • written 8 days ago by
schmince
• 0
3
votes
8
replies
676
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 9 days ago by
Chris Dean
▴ 410 • written 13 days ago by
sovrappensiero
▴ 100
1
vote
1
reply
667
views
Save experiment with batch effects - Protein microarray
statistics
protein-array
batch-effect
updated 29 days ago by
Ram
43k • written 4.4 years ago by
s.lima.diogenes
▴ 10
1
vote
5
replies
663
views
Duplicate marking, read names, and the SRA
SRA
MarkDuplicates
updated 26 days ago by
GenoMax
142k • written 26 days ago by
Luka
• 0
6
votes
8
replies
660
views
BRAKER3 genome annotation
annotation
BRAKER3
genome
updated 28 days ago by
dariober
14k • written 4 weeks ago by
manaswiniparija3
▴ 40
5
votes
5
replies
657
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 12 days ago by
Mbofire
• 0 • written 21 days ago by
Ming Tommy Tang
★ 3.9k
0
votes
4
replies
655
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
26 days ago by
Kai Xin
• 0
2
votes
2
replies
646
views
Batch correction for DE analysis
batch-correction
mRNA
RNA-seq
DEGs
MDSplot
updated 29 days ago by
Ram
43k • written 2.7 years ago by
Yoonji
▴ 10
0
votes
1
reply
646
views
Job:
Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Experience in RNA-seq, CADD & Deep Learning Molecular Generation
search
job
updated 10 days ago by
GenoMax
142k • written 11 days ago by
tulip
• 0
1
vote
5
replies
638
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode
MGI
DNBelab
single-cell
updated 22 days ago by
atowns21
• 0 • written 3 months ago by
benjamin.pyenson
• 0
3
votes
5
replies
631
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
23 days ago by
n_navy
• 0
2
votes
5
replies
630
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis
MEGA
updated 25 days ago by
Mensur Dlakic
★ 27k • written 26 days ago by
Giorgio
• 0
4
votes
7
replies
628
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
16 days ago by
e.r.zakiev
▴ 210
3
votes
1
reply
627
views
What is the normalization status of metabric data?
metabric
normalization
microarray
cbioportal
updated 28 days ago by
etiennedanis
▴ 20 • written 20 months ago by
DareDevil
★ 4.3k
0
votes
7
replies
625
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 13 days ago by
LChart
3.9k • written 16 days ago by
kl
▴ 10
0
votes
4
replies
614
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 25 days ago by
ATpoint
82k • written 26 days ago by
rheab1230
▴ 140
3
votes
9
replies
607
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 21 days ago by
Istvan Albert
100k • written 23 days ago by
Κοσμάς
• 0
900 results • Page
6 of 18
Recent Votes
A: ensembl gene id
A: How to deal with the case that one gene symbol matches multiple ensembl ids?
Answer: DESeq2 error
Answer: Using ggplotly in R
Comment: How to calculate coverage of Nanopore long read data?
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Calculate allelic frequency from VEP output vcf file
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Comment: ggrepel function: geom_text_repel()
by
ntsopoul
▴ 60
The plot looks confusing, chek the documentation there is an attribute called force. If you reduce the value you should get better results.…
Comment: Sequencing Depth (Read Depth) Calculations
by
LucisTheFather
• 0
Understood! Gonna try those two!
Comment: Sequencing Depth (Read Depth) Calculations
by
LucisTheFather
• 0
Thank u very much!
Comment: How to extract cells of different species after mapping with combined genome?
by
GenoMax
142k
You have used the tag `snRNAseq`. I am not familiar with singleron tech but if you have sequence data you may be able to use `xenome` or `b…
Comment: bbmerge (bbmap) ~ error with insert size file output
by
GenoMax
142k
It may be best to go back to the original data and then do `bbmerge.sh` on it to get original insert size estimates (before any operations …
Comment: bbmerge (bbmap) ~ error with insert size file output
by
chrisk
• 0
Hi Brian, Thank you and apologies for the extra future revision works. Out of curiosity we disabled neural networks 'nn=f' and the file o…
Comment: bbmerge (bbmap) ~ error with insert size file output
by
chrisk
• 0
Hi Genomax, This is the thread: https://www.biostars.org/p/9582467/ Cheers, Chris
Comment: Inquiry about deseq2 transformation
by
Chen
• 0
that's helpful, thanks :)
Comment: bbmerge (bbmap) ~ error with insert size file output
by
Brian Bushnell
20k
Ah, this is a little embarrassing; those are the vectors for the neural network. I overloaded a field that was being used for the insert s…
Comment: Annotating file using bcftools
by
kl
▴ 10
Thanks - I corrected it. It doesn't seem to annotate. I converted to binary after which is what is shown below. It is not the output I want…
Comment: Filtering VCF files based on VAF giving incorrect results
by
Arton
▴ 10
These are valid questions. Does your code address the concerns you've raised? From what I understand, FilterVcf is primarily designed for h…
Answer: Calculate allelic frequency from VEP output vcf file
by
ramiro.barrantes
• 0
Found the answer here!! https://github.com/Illumina/strelka/blob/master/docs/userGuide/README.md#somatic Although this leads to a str…
Comment: Using VEP annotation output as the input for a second VEP annotation
by
Ram
43k
That's not a valid reason to delete the post. If that information was sensitive, posting it here was a mistake in the first place. I don't …
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
by
marco.barr
▴ 120
Hi, regardless of how you generated the data whether with DESeq2 or other pipeline, your differential expression matrix can be used as inpu…
Comment: Filtering VCF files based on VAF giving incorrect results
by
Pierre Lindenbaum
161k
> Do you think my commands were correct? I'm not familiar enough with this bcftools syntax. but what if there is no AD, what if both…
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