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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
26
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
1 hour ago by
biocellbio
• 0
0
votes
0
replies
40
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
updated 3 hours ago by
Ram
43k • written 4 hours ago by
Guille
• 0
0
votes
0
replies
48
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 6 hours ago by
Ram
43k • written 7 hours ago by
vanbelj
▴ 40
0
votes
0
replies
47
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
updated 5 hours ago by
GenoMax
141k • written 7 hours ago by
hagl
▴ 10
0
votes
0
replies
84
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
13 hours ago by
HarperReed
• 0
1
vote
0
replies
62
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
16 hours ago by
KABILAN
▴ 50
0
votes
0
replies
63
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 2 hours ago by
Ram
43k • written 16 hours ago by
SineWave
• 0
0
votes
0
replies
64
views
RNA-seq: full length gene
RNA-seq
updated 6 hours ago by
Ram
43k • written 16 hours ago by
Nargis
• 0
0
votes
0
replies
60
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
18 hours ago by
turcoa1
• 0
0
votes
0
replies
74
views
Designing single-stable RNA molecules
structure
RNA
1 day ago by
Edna
• 0
0
votes
0
replies
85
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
1 day ago by
simplitia
▴ 130
0
votes
1
reply
123
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 1 day ago by
ATpoint
82k • written 1 day ago by
AaronJaime
• 0
0
votes
0
replies
86
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
1 day ago by
avocado123
• 0
0
votes
0
replies
76
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
1 day ago by
Emily
▴ 10
1
vote
0
replies
96
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
1 day ago by
rohitsatyam102
▴ 850
0
votes
0
replies
80
views
how to read graph_test output of monocle 3
monocle3
1 day ago by
synat.keam
▴ 100
0
votes
1
reply
412
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 1 day ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
0
votes
0
replies
94
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
1 day ago by
Aspire
▴ 300
0
votes
3
replies
196
views
Highest variable features in single cell data
single-cell
updated 2 hours ago by
bk11
★ 2.4k • written 1 day ago by
Kazo
• 0
1
vote
2
replies
228
views
PCA plot
DESeq2
PCAplot
updated 13 hours ago by
ATpoint
82k • written 1 day ago by
Aaliya
▴ 10
0
votes
0
replies
116
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
1 day ago by
4fzcgueyp5
• 0
0
votes
2
replies
224
views
Annovar using R package
Annovar
gnomAD
R
1 day ago by
DKA
▴ 40
0
votes
5
replies
295
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 1 day ago by
GenoMax
141k • written 2 days ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
131
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 2 days ago by
Ram
43k • written 2 days ago by
glaciya2018
• 0
0
votes
0
replies
266
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
2 days ago by
pramach1
▴ 40
0
votes
1
reply
142
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 2 days ago by
Sofia
• 0 • written 2 days ago by
mawigoj318
• 0
0
votes
0
replies
133
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
2 days ago by
salias
• 0
0
votes
4
replies
251
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
1 day ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
114
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 2 days ago by
Ram
43k • written 2 days ago by
newuser2024
• 0
1
vote
2
replies
203
views
alignment result
RNA-seq
samtools
hisat2
1 day ago by
ahmad.sajad4541
• 0
0
votes
0
replies
95
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 2 days ago by
Ram
43k • written 2 days ago by
Jeyong
• 0
0
votes
0
replies
106
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
2 days ago by
Kash
▴ 110
0
votes
1
reply
149
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 2 days ago by
Mensur Dlakic
★ 27k • written 3 days ago by
benguyarenbeyaz98
• 0
0
votes
2
replies
239
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 2 days ago by
Ram
43k • written 3 days ago by
v.berriosfarias
▴ 140
2
votes
9
replies
825
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 2 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
11
replies
482
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
22 hours ago by
atowns21
• 0
0
votes
1
reply
154
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 3 days ago by
bk11
★ 2.4k • written 3 days ago by
alphaflylizard
• 0
0
votes
0
replies
95
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
3 days ago by
ohtang7
▴ 40
0
votes
1
reply
156
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 3 days ago by
GenoMax
141k • written 3 days ago by
Srinka
▴ 20
0
votes
5
replies
298
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
2 days ago by
njornet
▴ 20
0
votes
0
replies
88
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 3 days ago by
Ram
43k • written 3 days ago by
SHREYA
• 0
0
votes
0
replies
97
views
Merging replicates from Encode project
CHIP-seq
encode
3 days ago by
Nurken
• 0
1
vote
3
replies
211
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
3 days ago by
WouterDeCoster
47k
1
vote
3
replies
250
views
some error in building kraken2 database
metagenome
kraken2
2 days ago by
Art1ess
• 0
0
votes
1
reply
133
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 3 days ago by
bk11
★ 2.4k • written 3 days ago by
Susmita Mandal
▴ 110
1
vote
1
reply
167
views
Failed kmer content
kmer
illumina
ngs
updated 3 days ago by
Ram
43k • written 3 days ago by
Kasturi
• 0
0
votes
0
replies
86
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 3 days ago by
Ram
43k • written 3 days ago by
SSSJec
• 0
0
votes
1
reply
143
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 4 days ago by
Ram
43k • written 4 days ago by
Cameron.walker9900
• 0
0
votes
8
replies
313
views
Error in cnetplot enrichplot package
R
updated 4 days ago by
Ram
43k • written 4 days ago by
Farhad
• 0
0
votes
0
replies
108
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 4 days ago by
Ram
43k • written 4 days ago by
maxime.policarpo
▴ 200
1,000 results • Page
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Recent Votes
Comment: Create a new bed file with all pairwise combinations between two other bed files
Answer: Create a new bed file with all pairwise combinations between two other bed files
Answer: Create a new bed file with all pairwise combinations between two other bed files
Answer: Create a new bed file with all pairwise combinations between two other bed files
Answer: Trimming tools - your experience please?
Answer: Trimming tools - your experience please?
Answer: Trimming tools - your experience please?
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There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
Comment: Create a new bed file with all pairwise combinations between two other bed files
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Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files
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J
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Thank you Pierre! I'll try this out with my full data set.
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I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
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You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
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Please include a link when you are recommending a tool. There can be programs with similar names.
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Check out clustergrammer from Avi Ma'ayan's lab.
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Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
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jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
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I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
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