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539 results • Page
3 of 11
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
154
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
8 days ago by
chemokine-1
▴ 10
0
votes
4
replies
494
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
7 days ago by
feather-W
• 0
0
votes
2
replies
217
views
Bedmethyl file format
bedmethyl
methylation
updated 8 days ago by
GenoMax
141k • written 8 days ago by
njornet
▴ 20
0
votes
0
replies
167
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
8 days ago by
Ali
• 0
2
votes
4
replies
312
views
SnpEff annotates coding duplication as intronic?
snpeff
8 days ago by
kirill.zaslavsky
• 0
0
votes
2
replies
245
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
8 days ago by
mropri
▴ 150
0
votes
0
replies
143
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames
RNA-Seq
WGCNA
unique
8 days ago by
shasabhi1
• 0
0
votes
0
replies
133
views
How to summarize dbCAN3 results
dbCAN
CAZy
CAZyme
dbCAN3
dbCAN2
8 days ago by
Nishat
• 0
0
votes
0
replies
159
views
what exactly is a k-mer table (remora)?
remora
basecall
8 days ago by
anne
• 0
1
vote
1
reply
175
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 8 days ago by
dsull
★ 5.8k • written 8 days ago by
niruf
• 0
0
votes
0
replies
141
views
GWAS Phenotypes
GWAS
9 days ago by
solomoncharles77
▴ 90
0
votes
2
replies
314
views
GSEA analysis in R
GSEA
R
Arabidopsis
7 days ago by
Sudip
• 0
0
votes
0
replies
122
views
Add geno header to VariantAnnotation objects
nichenet
scRNA-seq
9 days ago by
QX
• 0
2
votes
5
replies
436
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
8 days ago by
Bikram Kumar
• 0
0
votes
2
replies
256
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 8 days ago by
Ram
43k • written 9 days ago by
David
• 0
1
vote
2
replies
265
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
8 days ago by
bioinfo
▴ 150
0
votes
1
reply
192
views
How to get the reference panel sites for TOPMed hg37 and 38
Imputation
updated 9 days ago by
bk11
★ 2.3k • written 9 days ago by
sinhas
• 0
0
votes
1
reply
208
views
merging Seurat objects after SCT
Seurat
SCT
updated 9 days ago by
Ram
43k • written 9 days ago by
michelle.swarovski
• 0
0
votes
1
reply
201
views
Two databases: Human Microbiome Project and MGnify
Microbiome
databases
updated 9 days ago by
GenoMax
141k • written 9 days ago by
haiying.kong
▴ 360
0
votes
2
replies
263
views
RNAseq 1 control 2 different treatment
RNA-seq
9 days ago by
matteo.levorato
• 0
1
vote
0
replies
143
views
Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
Gene-ontology
RNA-seq
R
updated 9 days ago by
Ram
43k • written 9 days ago by
Oscar
▴ 10
0
votes
0
replies
152
views
How should I make kallisto indexes?
kallisto
updated 9 days ago by
GenoMax
141k • written 9 days ago by
bioinfo
▴ 150
2
votes
0
replies
202
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
10 days ago by
Alexander
▴ 220
1
vote
1
reply
181
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 10 days ago by
GenoMax
141k • written 10 days ago by
eesiribloom
▴ 80
0
votes
0
replies
137
views
Automated internal stop codon checker
ORF
stopcodon
internal
virus
10 days ago by
Balazs Horvath
▴ 10
0
votes
0
replies
142
views
Repeat expansion identification tools for long-read data
fragilex
repeatexpansion
long-read
fmr1
10 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
151
views
FreeBayes detection capacity
reads
freebayes
long
10 days ago by
quentinperriere
• 0
0
votes
2
replies
244
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
8 days ago by
DKA
▴ 40
0
votes
0
replies
161
views
Plotting heatmap of genes in each samples scRNA in Seurat
scRNA
heatmap
10 days ago by
Hien
• 0
0
votes
2
replies
286
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
8 days ago by
Koketso
• 0
0
votes
0
replies
189
views
Novel cyclic peptide structure prediction
protein
structure-prediction
alphafold
peptide
updated 10 days ago by
Ram
43k • written 11 days ago by
menyawino
• 0
1
vote
3
replies
345
views
Ensembl gene id conversion
biomart
ensembl
updated 9 days ago by
ATpoint
82k • written 11 days ago by
naveedhasan2000
• 0
1
vote
2
replies
314
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 9 days ago by
Istvan Albert
100k • written 11 days ago by
Jiang
• 0
0
votes
0
replies
188
views
Core SNP tree VS. concatenated core genome tree
phylogenetic
tree
SNP
12 days ago by
YiweiZhu
▴ 30
0
votes
2
replies
315
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
11 days ago by
O.rka
▴ 710
0
votes
6
replies
548
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
9 days ago by
Dunois
★ 2.5k
4
votes
7
replies
543
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 11 days ago by
Ram
43k • written 12 days ago by
AHerik
▴ 20
0
votes
0
replies
186
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 12 days ago by
GenoMax
141k • written 12 days ago by
zec018
• 0
0
votes
0
replies
193
views
SeuratDisk: including "counts" dataset in conversion to AnnData
Seurat
SeuratDisk
AnnData
updated 12 days ago by
Ram
43k • written 12 days ago by
roussine
▴ 10
0
votes
0
replies
182
views
I am getting more annotation hits from HOMER than I have actual peaks. Is that normal?
ATAC-seq
HOMER
12 days ago by
Ronin
• 0
4
votes
13
replies
860
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 8 days ago by
BioinfGuru
★ 1.7k • written 13 days ago by
matteo.levorato
• 0
2
votes
1
reply
245
views
VEP annotation --per_gene allele choice
VEP
updated 12 days ago by
Ram
43k • written 12 days ago by
atariw
▴ 10
0
votes
2
replies
282
views
Are GeneExpression Subtype annotations removed from TCGA-GBM?
tcga-gbm
subtyping
tcga
updated 12 days ago by
Zhenyu Zhang
★ 1.2k • written 13 days ago by
Apollonia
• 0
1
vote
1
reply
244
views
RNA seq normalization and gene gene correlation
rna-seq
pearson-correlation
vst
updated 12 days ago by
Ram
43k • written 13 days ago by
Fish
• 0
0
votes
0
replies
184
views
Snakemake fails to find conda in PBS
snakemake
13 days ago by
yixinzeng
• 0
0
votes
0
replies
188
views
KaryoPlot: Gene coverage over centromeric regions
Gene
coverage
Centromere
Bedtools
13 days ago by
Mary
• 0
0
votes
0
replies
180
views
Protein stability analysis
mutation
analysis
13 days ago by
marco.barr
▴ 80
1
vote
4
replies
388
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics
htseq-count
RNA-Seq
NGS
hisat2
updated 12 days ago by
BioinfGuru
★ 1.7k • written 13 days ago by
Morteza
• 0
3
votes
1
reply
264
views
how to change the gene header names in a fasta file?
fasta
bioawk
awk
seqkit
updated 13 days ago by
Ram
43k • written 13 days ago by
rj.rezwan
• 0
0
votes
0
replies
170
views
Multiple Spike-Ins
MeRIP
Spike-In
13 days ago by
Adam
▴ 20
539 results • Page
3 of 11
Recent Votes
discoSnp - reference-free finding of isolated SNPs from non assembled reads
Comment: Figures are disappeared from html report of SnpEff
Answer: Figures are disappeared from html report of SnpEff
Comment: How to trim transcripts using information from NCBI contamination screen report
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
A: What is the VEP Impact column?
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Recent Awards •
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Popular Question
to
maxime.policarpo
▴ 200
Popular Question
to
Hamtaro
▴ 50
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Nicolas Rosewick
11k
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Assa Yeroslaviz
★ 1.8k
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Recent Replies
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
GenoMax
141k
At this point you should email NCBI help desk and ask them this question. If you get an answer then please post it back in this thread.
Comment: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the javascript in your html is deprecated or your firefox is just tool old.
Comment: Why gatk VariantAnnotator required bam and coverage files
by
Pierre Lindenbaum
161k
> I would like to ask why they may require the bam file for this function? hum.. if you want to add the coverage, where do you think gatk …
Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴ 30
By following above approach I got this ![enter image description here][1] [1]: /media/images/b47490eb-d4c4-4f39-a7b2-f5b7b6b8
Comment: Highest variable features in single cell data
by
Kazo
• 0
I apologize for the confusion. What I meant to say is that, for example, the Trbv17 gene appears among the variable genes. However, when I …
Answer: why renaming Idents in Seurat object doesn't work?
by
Assa Yeroslaviz
★ 1.8k
I manage to find a workwround, but I don't understand what I did wrong here. my solution was to extract the cluster column as vector and…
Answer: Finding orthologs between genome error
by
Adrian Altenhoff
★ 1.1k
Hi, thanks for letting us know. In a recent software update, we introduced a problem with the written splice information in the cached …
Comment: Fetch table from clinvar database according to a list of rsid
by
ashaneev07
▴ 20
so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Sure, I'll inquire about the version of Rsubread. I'll keep you posted if it works :) Thanks
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Yeah, let me show you my featureCounts result, it looks like this. It's too low. [1]: /media/images/eb8293fe-e6ae-4b02-92e2-0ba2075b
Comment: Adding CB tag to bam file
by
Pierre Lindenbaum
161k
samtools addreplacerg is for read groups. This is not what OP asked.
Comment: Adding CB tag to bam file
by
Maria
• 0
When I try ``` samtools addreplacerg -r "@CB\tID:$cell" -o $cell.bam $LINE``` the CB tag gets add to the header, but the tag in every line …
Answer: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the remote website providing the javascript or/and the images is down or you're now behind a proxy. Check the firefox console: https://fire…
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