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116,730 results • Page
4 of 2335
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
175
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
7 days ago by
simplitia
▴ 130
1
vote
1
reply
226
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 7 days ago by
ATpoint
82k • written 7 days ago by
AaronJaime
• 0
0
votes
2
replies
294
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 7 days ago by
GenoMax
142k • written 7 days ago by
Begonia_pavonina
▴ 150
0
votes
3
replies
380
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
2 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
5 days ago by
Francesco
▴ 10
1
vote
7
replies
487
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 3 days ago by
bk11
★ 2.4k • written 7 days ago by
starswillfade
▴ 10
0
votes
0
replies
164
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 7 days ago by
Ram
43k • written 7 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
160
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
7 days ago by
Emily
▴ 10
1
vote
0
replies
171
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
7 days ago by
rohitsatyam102
▴ 850
0
votes
0
replies
155
views
how to read graph_test output of monocle 3
monocle3
7 days ago by
synat.keam
▴ 100
1
vote
0
replies
205
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
7 days ago by
Assaf
▴ 10
0
votes
1
reply
499
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 7 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
7 days ago by
QX
• 0
2
votes
1
reply
237
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 7 days ago by
Adrian Altenhoff
★ 1.1k • written 8 days ago by
hemantcnaik
• 0
0
votes
0
replies
152
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
7 days ago by
Aspire
▴ 330
2
votes
5
replies
347
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
4 days ago by
analyst
▴ 30
0
votes
3
replies
301
views
Highest variable features in single cell data
single-cell
updated 6 days ago by
bk11
★ 2.4k • written 8 days ago by
Kazo
▴ 10
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
374
views
PCA plot
DESeq2
PCAplot
updated 4 days ago by
LauferVA
4.2k • written 8 days ago by
Aaliya
▴ 10
4
votes
4
replies
442
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 5 days ago by
BioinfGuru
★ 1.7k • 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
151
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
334
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 10 days ago by
Mensur Dlakic
★ 27k • written 10 days ago by
emmanouil.a
▴ 120
0
votes
2
replies
262
views
Annovar using R package
Annovar
gnomAD
R
7 days ago by
DKA
▴ 40
0
votes
2
replies
238
views
Creating Synthetic Sequences for a ML Model
DNA
ML
updated 8 days ago by
Mensur Dlakic
★ 27k • written 8 days ago by
biochugs
• 0
8
votes
8
replies
628
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
857
views
Adding CB tag to bam file
samtools
bam
updated 8 days ago by
Pierre Lindenbaum
161k • written 14 days ago by
Maria
• 0
1
vote
10
replies
974
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
8 days ago by
DKA
▴ 40
0
votes
2
replies
824
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 8 days ago by
barslmn
★ 2.1k • written 2.8 years ago by
jhy
▴ 10
0
votes
5
replies
369
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 7 days ago by
GenoMax
142k • written 8 days ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
146
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 8 days ago by
Ram
43k • written 8 days ago by
glaciya2018
• 0
0
votes
0
replies
310
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
8 days ago by
pramach1
▴ 40
0
votes
13
replies
3.6k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 8 days ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
0
votes
1
reply
169
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 8 days ago by
Sofia
• 0 • written 8 days ago by
mawigoj318
• 0
0
votes
0
replies
149
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
8 days ago by
salias
• 0
4
votes
7
replies
495
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 8 days ago by
dsull
★ 5.9k • written 9 days ago by
VITALA
• 0
0
votes
5
replies
364
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 5 days ago by
Istvan Albert
100k • written 8 days ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
127
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 8 days ago by
Ram
43k • written 9 days ago by
newuser2024
• 0
1
vote
2
replies
246
views
alignment result
RNA-seq
samtools
hisat2
8 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
122
views
News:
hands-on introduction to generalized linear models (GLMs) using R
Generalized-Linear-Models
GLM
R
updated 8 days ago by
Ram
43k • written 9 days ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
235
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
8 days ago by
mropri
▴ 150
2
votes
2
replies
237
views
HaplotypeCaller - only SNPs
HaplotypeCaller
GATK
updated 9 days ago by
analyst
▴ 30 • written 9 days ago by
lorena9132
• 0
0
votes
0
replies
117
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
9 days ago by
Kash
▴ 110
7
votes
2
replies
285
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 9 days ago by
geneontologyhelp
▴ 390 • written 10 days ago by
catherine.teyssier
• 0
1
vote
1
reply
221
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting
blast
updated 9 days ago by
Istvan Albert
100k • written 10 days ago by
Abeer
• 0
2
votes
4
replies
334
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 9 days ago by
swbarnes2
14k • written 10 days ago by
dxj294
• 0
0
votes
1
reply
165
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 9 days ago by
Mensur Dlakic
★ 27k • written 9 days ago by
benguyarenbeyaz98
• 0
2
votes
2
replies
295
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 8 days ago by
Ram
43k • written 9 days ago by
v.berriosfarias
▴ 140
3
votes
1
reply
238
views
Seurat merge and batch correction
Seurat
updated 9 days ago by
Ram
43k • written 10 days ago by
sooni
▴ 20
116,730 results • Page
4 of 2335
Recent Votes
Comment: How to Calulate Allele Frequency from a VCF File?
Answer: Introduce SNPs on FASTA
Answer: how to split multi-fasta file into single fasta file named by header
How to Calulate Allele Frequency from a VCF File?
Answer: allele frequency in VCF
Answer: Two references 1. genome 2. plasmid for bowtie2
A: Iterating through paired-end reads in samtools / pysam
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Recent Replies
Comment: Introduce SNPs on FASTA
by
Riccardo
▴ 10
Thank you very much for your answer!
Comment: how to split multi-fasta file into single fasta file named by header
by
rsieber
▴ 10
This is great also for multiline fastas
Comment: how to split multi-fasta file into single fasta file named by header
by
rsieber
▴ 10
This only works for the first line of sequences.
Answer: What purposes can TPM values be used for?
by
b.contreras.moreira
▴ 180
In case it helps: https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units
Comment: What analysis suitable to identify similarly expressed genes between two samples
by
alifafiq1
• 0
Thank you @AT point. I was planning to use DESeq2 and use the alternate hypothesis (lessAbs) too considering that is the only package that …
Comment: Does comparing two different groups to a common third group introduce bias in th
by
ATpoint
82k
Note that by basic algebra A vs C and B vs C is the same as A vs B, so you might rethink your analysis to answer your question in a much si…
Comment: RNAseq one control two conditions, shared and exclusive genes
by
Mohamed Abderrahmane
▴ 20
Yes, why not? If it works for you like that, bingo!
Answer: Does comparing two different groups to a common third group introduce bias in th
by
christopher medway
▴ 450
You are testing groups A and B to a common baseline (C) - I don't see that there is anything wrong with doing that. It is a fairly common a…
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by
clairechung112
• 0
Hi. I guess it is solved by now, but as I did not find the answer immediately online, here is the answer I posted on a relevant question: h…
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by
clairechung112
• 0
A late reply, but I just solved exactly the same error upon a request in the team. Please see if it helps in case anyone meets the same err…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
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▴ 390
Was the spike-in a commercial product, e.g., from Zymo? Can you provide more information about what cells or DNA was spiked into your samp…
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Note that, in place of `sort-bed - | uniq -`, you can pass the `--unique` option to `sort-bed`. The input is not strictly a BED6 file, but…
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3.9k
Imputation takes what? A day or two of compute time? Just re-do it.
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Thanks. Really appreciate your help with this. This site is such a great resource. The methods aren't totally clear on how they're gettin…
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142k
It is possible that these drugs may not have been directly used in TCGA. Authors could have looked for mutations known to be acted on by th…
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