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116,756 results • Page
4 of 2336
Sort: Rank
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Votes
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0
votes
1
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750
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 6 days ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
3
votes
2
replies
298
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 5 days ago by
i.sudbery
19k • written 8 days ago by
vanbelj
▴ 40
0
votes
0
replies
122
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 5 days ago by
dariober
14k • written 6 days ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
302
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 6 days ago by
ATpoint
82k • written 6 days ago by
Francesco
▴ 10
0
votes
0
replies
139
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
6 days ago by
tnminh89
▴ 10
0
votes
0
replies
144
views
Filter low express genes in microarray data
microarray
6 days ago by
Chris
▴ 260
0
votes
1
reply
335
views
absolute path for symbolic links in Snakefile
Snakemake
updated 6 days ago by
Jesse
▴ 740 • written 15 days ago by
yifangt86
▴ 60
0
votes
2
replies
357
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 6 days ago by
Jesse
▴ 740 • written 9 days ago by
Broccoli
• 0
4
votes
3
replies
368
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 7 days ago by
Arup Ghosh
3.2k • written 8 days ago by
chaco001
▴ 40
1
vote
3
replies
395
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
updated 5 days ago by
Mensur Dlakic
★ 27k • written 7 days ago by
O.rka
▴ 710
0
votes
2
replies
260
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
7 days ago by
Guille
• 0
4
votes
2
replies
304
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
5 days ago by
pairedttest
▴ 10
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 7 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
0
votes
0
replies
570
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
7 days ago by
biocellbio
• 0
4
votes
8
replies
655
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 7 days ago by
Alex Reynolds
35k • written 8 days ago by
J
▴ 10
4
votes
7
replies
709
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 7 days ago by
dsull
★ 6.0k • written 11 days ago by
qudrat.nii
▴ 10
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 8 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
3
votes
2
replies
331
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 8 days ago by
dsull
★ 6.0k • written 8 days ago by
Aaliya
▴ 10
3
votes
0
replies
212
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 7 days ago by
Ram
43k • written 8 days ago by
Claire Watson
▴ 60
0
votes
2
replies
290
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 7 days ago by
Ram
43k • written 8 days ago by
The_PyPanda
▴ 10
0
votes
0
replies
206
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
8 days ago by
HarperReed
• 0
3
votes
3
replies
311
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 8 days ago by
GenoMax
142k • written 8 days ago by
sapuizait
▴ 10
1
vote
0
replies
161
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
8 days ago by
KABILAN
▴ 70
0
votes
0
replies
177
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 7 days ago by
Ram
43k • written 8 days ago by
SineWave
• 0
0
votes
0
replies
173
views
RNA-seq: full length gene
RNA-seq
updated 8 days ago by
Ram
43k • written 8 days ago by
Nargis
• 0
1
vote
7
replies
504
views
gvcf joint calling
WES
GATK
VCF
gVCF
6 days ago by
zihanss
• 0
0
votes
0
replies
157
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
8 days ago by
turcoa1
• 0
3
votes
3
replies
309
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 8 days ago by
swbarnes2
14k • written 9 days ago by
M
• 0
0
votes
0
replies
167
views
Designing single-stable RNA molecules
structure
RNA
8 days ago by
Edna
• 0
0
votes
0
replies
178
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
8 days ago by
simplitia
▴ 130
1
vote
1
reply
231
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 8 days ago by
ATpoint
82k • written 8 days ago by
AaronJaime
• 0
0
votes
2
replies
297
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 8 days ago by
GenoMax
142k • written 9 days ago by
Begonia_pavonina
▴ 150
0
votes
3
replies
389
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
4 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
2
replies
340
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
6 days ago by
Francesco
▴ 10
1
vote
7
replies
503
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 5 days ago by
bk11
★ 2.4k • written 9 days ago by
starswillfade
▴ 10
0
votes
0
replies
165
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 8 days ago by
Ram
43k • written 9 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
161
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
9 days ago by
Emily
▴ 10
1
vote
0
replies
173
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
9 days ago by
rohitsatyam102
▴ 850
0
votes
0
replies
157
views
how to read graph_test output of monocle 3
monocle3
9 days ago by
synat.keam
▴ 100
1
vote
0
replies
208
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
9 days ago by
Assaf
▴ 10
0
votes
1
reply
503
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 9 days ago by
ginellegrenier
• 0 • written 5 months ago by
Clayton
• 0
3
votes
4
replies
358
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
8 days ago by
QX
• 0
2
votes
1
reply
242
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 9 days ago by
Adrian Altenhoff
★ 1.1k • written 10 days ago by
hemantcnaik
• 0
0
votes
0
replies
154
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
9 days ago by
Aspire
▴ 330
2
votes
5
replies
370
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
5 days ago by
analyst
▴ 30
0
votes
3
replies
314
views
Highest variable features in single cell data
single-cell
updated 7 days ago by
bk11
★ 2.4k • written 9 days ago by
carolofharvest
▴ 30
0
votes
1
reply
228
views
Network Alignment
plugin
Cytoscape
CytoMCS
updated 9 days ago by
Scooter
▴ 280 • written 10 days ago by
Akash D
▴ 40
2
votes
4
replies
2.4k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi
metagenomics
centrifuge
gi_taxid_nucl.dmp
taxonomy
updated 9 days ago by
ZhangYuanfeng
• 0 • written 2.4 years ago by
Frazier Baker
• 0
1
vote
3
replies
385
views
PCA plot
DESeq2
PCAplot
updated 5 days ago by
LauferVA
4.2k • written 9 days ago by
Aaliya
▴ 10
5
votes
5
replies
560
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 23 hours ago by
Mbofire
• 0 • written 9 days ago by
Ming Tommy Tang
★ 3.9k
116,756 results • Page
4 of 2336
Recent Votes
Answer: Design matrix Differential expression analysis
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Answer: RNA velocity for smart-seq2 dataset
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Comment: Design matrix Differential expression analysis
by
SHN
▴ 40
Thank you for your explanation. I am working on the cell lines and I am investigating the effect of the treatment on the expression level, …
Answer: Issues with Mixture file when using CIBERSORTx
by
vjanve
• 0
I ran into same issue of "duplicated gene symbol(s)": 1: In CIBERSORTxFractions(sigmatrix = sigmatrix, mixture = mixture, : 22292 dup…
Comment: creating batch colum for batch correction
by
Expert
▴ 10
Thank you for your response. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are ind…
Comment: creating batch colum for batch correction
by
ATpoint
82k
Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write dow…
Comment: Pindel Segmentation Fault Error
by
Ruqaiya
• 0
This the tool still problematic?
Comment: Segmentation error while using a tool
by
Ruqaiya
• 0
Thank you for the advice, i'll keep that in mind.
Comment: Segmentation error while using a tool
by
Ruqaiya
• 0
I am trying to reproduce some bioinformatics data from a research paper-[this paper][1] as i was asked to work on an MRSA bioinfo project, …
Answer: Segmentation error while using a tool
by
Mensur Dlakic
★ 27k
Most likely you didn't do anything wrong. Going by your previous post that you have only 8 GB of RAM, the most likely reason is the lack of…
Comment: Segmentation error while using a tool
by
Thanujay S
• 0
Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
Comment: Extracting mutation status from MAF files - TCGA
by
Thanujay S
• 0
Hey! Can you explain the question further? What have you tried?
Comment: Downloading older version of a tool
by
Ruqaiya
• 0
I tried the 2nd option only. I got the files of older version from the author but that version isn't working on my WSL, it's showing Segmen…
Comment: filtering before dada2
by
GenoMax
142k
> I encountered a significant decrease in the percentage of merged reads. You can check with `bbmerge.sh` from BBMap suite to see how many…
Comment: HCL database download
by
GenoMax
142k
Isn't the download link available above the plot: http://bis.zju.edu.cn/HCL/data/DGE/Adult-Transverse-Colon1_dge.txt.gz
Comment: fastq screen aligner no specified.
by
GenoMax
142k
You need to change this configuration file to point it to the location where the aligner executable can be found. So as an example followi…
Answer: Design matrix Differential expression analysis
by
Gordon Smyth
★ 7.1k
The expression levels do not change but the way that you have parametrized the expression levels does change. The two design matrices give…
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