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332 results • Page
2 of 7
Sort: Votes
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Views
Votes
Replies
1
vote
7
replies
585
views
Question regarding WGCNA
WGCNA
Network-construction
12 days ago by
deepak
• 0
1
vote
1
reply
267
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 21 days ago by
Ram
44k • written 21 days ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
290
views
permutation test in edgeR
rna-seq
edgeR
updated 29 days ago by
Gordon Smyth
★ 7.2k • written 6 weeks ago by
Netanel
• 0
1
vote
2
replies
289
views
Downloading full alignments from Pfam
pfam
16 days ago by
bef1
• 0
1
vote
1
reply
468
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 12 days ago by
Jaïr
• 0 • written 5 months ago by
NorbertK
▴ 10
1
vote
4
replies
435
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 11 days ago by
GenoMax
142k • written 4 weeks ago by
aniigodwinn
• 0
1
vote
2
replies
377
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 8 days ago by
Ram
44k • written 9 days ago by
t.fortunato.asquini
• 0
1
vote
2
replies
269
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 21 days ago by
Ram
44k • written 21 days ago by
Ravita
• 0
1
vote
1
reply
153
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 7 days ago by
Ram
44k • written 7 days ago by
kilcdincer
▴ 10
1
vote
2
replies
339
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
20 days ago by
Nafi
• 0
1
vote
0
replies
182
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
12 days ago by
eebloom
▴ 80
1
vote
1
reply
191
views
student
epitranscriptomics
updated 14 days ago by
ATpoint
82k • written 14 days ago by
useriwa
• 0
1
vote
2
replies
215
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
14 days ago by
robert.flynn.21
• 0
1
vote
0
replies
154
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
12 days ago by
Shae
▴ 10
1
vote
2
replies
378
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 3 hours ago by
finch
• 0 • written 3 months ago by
star
▴ 10
1
vote
1
reply
174
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 12 days ago by
andres.firrincieli
3.6k • written 12 days ago by
kacollier
▴ 30
1
vote
4
replies
362
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 6 days ago by
Juke34
8.6k • written 8 days ago by
Vijith
▴ 30
1
vote
1
reply
275
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 26 days ago by
ATpoint
82k • written 26 days ago by
AaronJaime
• 0
1
vote
0
replies
101
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
8 days ago by
tomas4482
▴ 400
1
vote
9
replies
462
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 11 days ago by
i.sudbery
19k • written 14 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
176
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 19 days ago by
Ram
44k • written 19 days ago by
marco.barr
▴ 130
1
vote
3
replies
463
views
PCA plot
DESeq2
PCAplot
updated 23 days ago by
LauferVA
4.2k • written 26 days ago by
Aaliya
▴ 10
1
vote
3
replies
306
views
Odd alignment question/finding
Alignment
updated 18 days ago by
barslmn
★ 2.2k • written 19 days ago by
poordumbsillyidiot
• 0
1
vote
1
reply
221
views
Failed kmer content
kmer
illumina
ngs
updated 28 days ago by
Ram
44k • written 28 days ago by
Kasturi
• 0
1
vote
2
replies
305
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
19 days ago by
rianna.collins
• 0
1
vote
2
replies
290
views
alignment result
RNA-seq
samtools
hisat2
26 days ago by
ahmad.sajad4541
• 0
1
vote
1
reply
53
views
Multiplexing for pooled CRISPR screen sequencing
multiplex
CRISPR-screen
Illumina
2 hours ago by
Tuấn Anh
• 0
1
vote
3
replies
387
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 23 days ago by
ATpoint
82k • written 24 days ago by
Francesco
▴ 10
1
vote
8
replies
577
views
Downsampling fastq file
downsample
fastq
21 days ago by
marco.barr
▴ 130
0
votes
0
replies
55
views
How does Kraken2 deal with poor read qualities?
kraken
qiime2
kraken2
qiime
updated 7 hours ago by
GenoMax
142k • written 8 hours ago by
Christopher
• 0
0
votes
2
replies
127
views
Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis of Spleen Samples from Different Conditions
Seurat
scRNA-Seq
Single-Cell
5 hours ago by
Shukai
• 0
0
votes
4
replies
414
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
8 days ago by
beginner123
• 0
0
votes
4
replies
188
views
Where to find old version of GATK best practice
gatk
5 hours ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
244
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 19 days ago by
GenoMax
142k • written 20 days ago by
mgranada3
▴ 30
0
votes
0
replies
49
views
Linking AMR Genes to Taxonomy in Soil Metagenomics
metagenomics
bacteria
wgs
AMR
resistome
updated 7 hours ago by
GenoMax
142k • written 7 hours ago by
LuciaNhu
• 0
0
votes
0
replies
130
views
Cox Model with interaction item interpretation
Cox
15 days ago by
Bine
▴ 60
0
votes
1
reply
220
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 28 days ago by
bk11
★ 2.5k • written 28 days ago by
alphaflylizard
• 0
0
votes
0
replies
157
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Long
• 0
0
votes
1
reply
101
views
How to hide label in layout file of MCscan (python version)
MCscan
updated 1 day ago by
GenoMax
142k • written 1 day ago by
jinyi
• 0
0
votes
0
replies
128
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 8 days ago by
Ram
44k • written 22 days ago by
atharvakarkare14
▴ 40
0
votes
2
replies
397
views
How to update R on ubuntu
installation
update
R
apt-get
22 days ago by
Bosberg
▴ 50
0
votes
0
replies
115
views
Normalizing AMR gene count data
abundance
RGI
updated 15 days ago by
Ram
44k • written 15 days ago by
arshad1292
▴ 100
0
votes
1
reply
210
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 11 days ago by
Ram
44k • written 11 days ago by
Shwetha
• 0
0
votes
0
replies
141
views
Mitogenomes gap closure and making circular genome
gapclosure
Mitogenomes
validation
circulargenome
16 days ago by
KHURRAM SHAHZAD
• 0
0
votes
0
replies
195
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 25 days ago by
Ram
44k • written 25 days ago by
SineWave
• 0
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 13 days ago by
Emanoelle
• 0 • written 5.8 years ago by
Elizabeth
▴ 30
0
votes
0
replies
116
views
lncRNA
tcga
lncrna
8 days ago by
jain72744
▴ 10
0
votes
0
replies
160
views
Use of ichor CNA
Dog
CNA
genome
5 days ago by
sainavyav22
• 0
0
votes
0
replies
177
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
26 days ago by
4fzcgueyp5
• 0
0
votes
0
replies
196
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
12 days ago by
Matvii Mykhailichenko
• 0
332 results • Page
2 of 7
Recent Votes
Comment: Problem in getting geo file through GEOQUERY
Answer: Question about samtools view flags (paired reads vs. properly paired reads)
Answer: Functional enrichment analysis for unique gene IDs
Comment: Super ehancers
Comment: Why does assigning genes with biomart give me different values than using a tran
Comment: Multiplexing for pooled CRISPR screen sequencing
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
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Recent Replies
Answer: Problem in getting geo file through GEOQUERY
by
ATpoint
82k
Code runs for me and finishes in seconds. Maybe some poor internet connection on your end. Just set the timeout to 9999999 and retry. If th…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c
by
ezz3
• 0
Thanks. I was wondering if that is the case but was having some issues understanding the transanno code which is written in rust and I don…
Answer: Multi-ploid data in ANGSD and NGSadmix
by
andersdetermig
▴ 20
1 ) I would not expect the haploid individuals to always cluster together but the model assumptions are violated. First of all the diploid…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c
by
Pierre Lindenbaum
161k
"Are you using correct reference?" may be your reference is not using the same chrM. see https://www.biostars.org/p/199796/#199803
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
shpak.max
▴ 50
Could you please elaborate on what you mean by passing -L or -V, i.e. what would the appropriate argument be for -L with UnifiedGenotyper f…
Answer: Add stats to the plot
by
Ghada
• 0
It works. I have added this code my_comparisons=list(c("HRSV", "HRSV_RBV")) plot + stat_compare_means(method = "wilcox.test",comparis…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
LChart
3.9k
I believe UnifiedGenotyper is a locus walker that sets `emitEmptySites() = False`. As such you will not see entries for positions that have…
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
Basically this is my code: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # # pkgs <- rowna…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
shpak.max
▴ 50
If that were the case, I would expect there not to be any uncalled sites in the vcf, yet there are a large number of sites with "." placeho…
Comment: Problem in getting geo file through GEOQUERY
by
bk11
★ 2.5k
It just runs fine for me with just a single line of code. library(GEOquery) GSE1145 <- getGEO("GSE1145", GSEMatrix=TRUE) …
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
Dave Carlson
★ 1.7k
I can't speak to UnifiedGenotyper, as it has been many years since GATK stopped supporting it, and I have not used it in a long time. But …
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
I want to get lot of files through code
Comment: Problem in getting geo file through GEOQUERY
by
GenoMax
142k
Query seems to be timing out. Try getting the file directly here: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1145/matrix/GSE1145-GP…
Comment: Add stats to the plot
by
Ghada
• 0
Thanks for the help. Unfortunately, did not work :( error in asserttat_group_columns_exists(data) : data should contain group1 and grou…
Comment: downloading chemical database from ChEMBL
by
GenoMax
142k
How about following https://www.ebi.ac.uk/chembl/web_components/explore/activities/ --> Select a compound --> Related Targets button --> D…
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