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116,748 results • Page
4 of 2335
Sort: Rank
Rank
Views
Votes
Replies
4
votes
2
replies
299
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
4 days ago by
pairedttest
▴ 10
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 6 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
0
votes
0
replies
568
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
649
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 6 days ago by
Alex Reynolds
35k • written 7 days ago by
J
▴ 10
4
votes
7
replies
693
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 6 days ago by
dsull
★ 6.0k • written 10 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 7 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
3
votes
2
replies
330
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 7 days ago by
dsull
★ 6.0k • written 7 days ago by
Aaliya
▴ 10
3
votes
0
replies
209
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 7 days ago by
Claire Watson
▴ 60
0
votes
2
replies
282
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 7 days ago by
Ram
43k • written 7 days ago by
The_PyPanda
▴ 10
0
votes
0
replies
206
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
7 days ago by
HarperReed
• 0
3
votes
3
replies
306
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 7 days ago by
GenoMax
142k • written 7 days ago by
sapuizait
▴ 10
1
vote
0
replies
160
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
7 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 7 days ago by
SineWave
• 0
0
votes
0
replies
173
views
RNA-seq: full length gene
RNA-seq
updated 7 days ago by
Ram
43k • written 7 days ago by
Nargis
• 0
1
vote
7
replies
494
views
gvcf joint calling
WES
GATK
VCF
gVCF
5 days ago by
zihanss
• 0
0
votes
0
replies
156
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
7 days ago by
turcoa1
• 0
3
votes
3
replies
304
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 7 days ago by
swbarnes2
14k • written 8 days ago by
M
• 0
0
votes
0
replies
166
views
Designing single-stable RNA molecules
structure
RNA
8 days ago by
Edna
• 0
0
votes
0
replies
177
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
8 days ago by
simplitia
▴ 130
1
vote
1
reply
229
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
296
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 8 days ago by
GenoMax
142k • written 8 days ago by
Begonia_pavonina
▴ 150
0
votes
3
replies
384
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
3 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
2
replies
333
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
6 days ago by
Francesco
▴ 10
1
vote
7
replies
490
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 4 days ago by
bk11
★ 2.4k • written 8 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 8 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
161
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
8 days ago by
Emily
▴ 10
1
vote
0
replies
172
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
8 days ago by
rohitsatyam102
▴ 850
0
votes
0
replies
157
views
how to read graph_test output of monocle 3
monocle3
8 days ago by
synat.keam
▴ 100
1
vote
0
replies
207
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
8 days ago by
Assaf
▴ 10
0
votes
1
reply
502
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 8 days ago by
ginellegrenier
• 0 • written 5 months ago by
Clayton
• 0
3
votes
4
replies
348
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
8 days ago by
QX
• 0
2
votes
1
reply
239
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 8 days ago by
Adrian Altenhoff
★ 1.1k • written 9 days ago by
hemantcnaik
• 0
0
votes
0
replies
154
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
8 days ago by
Aspire
▴ 330
2
votes
5
replies
350
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
4 days ago by
analyst
▴ 30
0
votes
3
replies
304
views
Highest variable features in single cell data
single-cell
updated 7 days ago by
bk11
★ 2.4k • written 8 days ago by
carolofharvest
▴ 30
0
votes
1
reply
222
views
Network Alignment
plugin
Cytoscape
CytoMCS
updated 8 days ago by
Scooter
▴ 280 • written 9 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 8 days ago by
ZhangYuanfeng
• 0 • written 2.4 years ago by
Frazier Baker
• 0
1
vote
3
replies
378
views
PCA plot
DESeq2
PCAplot
updated 5 days ago by
LauferVA
4.2k • written 8 days ago by
Aaliya
▴ 10
5
votes
5
replies
473
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 2 hours ago by
Mbofire
• 0 • written 8 days ago by
Ming Tommy Tang
★ 3.9k
0
votes
4
replies
2.7k
views
Lositan freezing when generating selection table
LOSITAN
updated 8 days ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 0
0
votes
0
replies
152
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
8 days ago by
4fzcgueyp5
• 0
2
votes
3
replies
337
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 11 days ago by
Mensur Dlakic
★ 27k • written 11 days ago by
emmanouil.a
▴ 120
0
votes
2
replies
263
views
Annovar using R package
Annovar
gnomAD
R
8 days ago by
DKA
▴ 40
0
votes
2
replies
239
views
Creating Synthetic Sequences for a ML Model
DNA
ML
updated 8 days ago by
Mensur Dlakic
★ 27k • written 9 days ago by
biochugs
• 0
8
votes
8
replies
631
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 8 days ago by
swbarnes2
14k • written 9 days ago by
Aaliya
▴ 10
1
vote
8
replies
864
views
Adding CB tag to bam file
samtools
bam
updated 8 days ago by
Pierre Lindenbaum
161k • written 15 days ago by
Maria
• 0
1
vote
10
replies
979
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
9 days ago by
DKA
▴ 40
0
votes
2
replies
826
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 9 days ago by
barslmn
★ 2.1k • written 2.8 years ago by
jhy
▴ 10
0
votes
5
replies
370
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 8 days ago by
GenoMax
142k • written 9 days ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
148
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 9 days ago by
Ram
43k • written 9 days ago by
glaciya2018
• 0
116,748 results • Page
4 of 2335
Recent Votes
Comment: No INFO/info value in headers
how to combine multiple RNAseq count files into a single dataframe in R and unix
Comment: Greatly speed up conda by using mamba
Greatly speed up conda by using mamba
Comment: Converting CRAM to FastQ
Parametric or non-parametric tests for qPCR significance testing between treatments?
Answer: Converting CRAM to FastQ
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Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
14k
Pictures of code are useless. You were told to paste the code and use the 0101 button. Can you explain why you decided not to do that? If…
Comment: Differential Expression Analysis using DESeq2 in R
by
Erina
• 0
![Here is the code I am using for the analysis][1] [1]: /media/images/8a511904-6ae8-47f5-b647-ee15b02b
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
by
swbarnes2
14k
In paired end sequencing, every read has a mate, and the flags all together tell you not only what is up with the read you are looking at, …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
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Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
According to the link: "When *generating* such filesets, PLINK 1.x defaults to swapping the alleles whenever A1's frequency is above (not …
Comment: TaxID mapping file
by
GenoMax
142k
nodesDB file should have been installed if you had used "Install" script for `blobtools` according to : https://blobtools.readme.io/docs/ta…
Comment: Parametric or non-parametric tests for qPCR significance testing between treatme
by
e.r.zakiev
▴ 210
obviously if the values are really sampled from a (quasi) normally-distributed values, then n doesn't matter, he could use t-test even with…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
Understood Thank you!
Comment: Converting CRAM to FastQ
by
GenoMax
142k
You can use any reference that you like at this point. Since you are planning to use GATK, you can get their version from the resource bund…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
![enter image description here][1]I was able to get my fastq files. I can see that my reference files are cached in a hts-ref directory but…
Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
14k
Okay, that shows us the problem, but not what we need to solve it. But, for instance, are you sure that period after the sample name shou…
Comment: Easy way to find out which allele is minor allele from bed file?
by
bk11
★ 2.4k
In the case of MAF = 0.5, I think A1 is still the minor allele. You can check the discussion in this [link][1]. [1]: https://groups.goo…
Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
Yes, but I think the problem is what to do when MAF = 0.5
Answer: Easy way to find out which allele is minor allele from bed file?
by
bk11
★ 2.4k
In Plink, A1 is usually a minor allele and A2 a major allele. .frq (basic allele frequency report) Produced by --freq. …
Comment: Raw counts using stringtie
by
GenoMax
142k
> Error parsing strand from GFF line Looking at this error and the listing of files in your directory it looks like you need to `gunzip` t…
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