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115 results • Page
2 of 3
Sort: Views
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Views
Votes
Replies
0
votes
2
replies
155
views
Error with goodSamplesGenes()
R
WGCNA
1 day ago by
bioinfo_enthusiast
• 0
1
vote
1
reply
154
views
Pool-Seq same as normal variant calling?
Pool-Seq
Variant-Calling
updated 2 days ago by
dthorbur
★ 1.7k • written 2 days ago by
andrebolerbarros
• 0
0
votes
1
reply
149
views
Autodock tools error - The requested operation requires lifting
Autodock
MGLTools
updated 3 days ago by
zx8754
11k • written 3 days ago by
DOMENICA ALEXANDRA
• 0
0
votes
1
reply
148
views
dbsnp flanks information
dbsnp
updated 2 days ago by
Pierre Lindenbaum
160k • written 2 days ago by
sskimvd
• 0
0
votes
1
reply
148
views
Karytotype color annotations
karyotype
annotations
chromosome
color
updated 2 days ago by
Pierre Lindenbaum
160k • written 3 days ago by
Mary
• 0
0
votes
0
replies
148
views
Cromwell slurm singularity call caching
cromwell
singularity
wdl
5 days ago by
asmariyaz23
▴ 10
0
votes
1
reply
146
views
NCBI gene data
Variants
NCBI
updated 3 days ago by
GenoMax
140k • written 3 days ago by
chandrakala.m
• 0
0
votes
1
reply
142
views
Cell communacations analysis. I only have the proteome of one type of cell
How
to
updated 2 days ago by
ATpoint
81k • written 2 days ago by
David Arturo
• 0
0
votes
0
replies
140
views
beta coefficient improves after doing mediation analysis
coefficient
mediation
beta
regression
5 days ago by
rheab1230
▴ 140
0
votes
1
reply
140
views
How to perform GO enrichment analysis for assembled sequence ?
GO-enrichment
Gene-Ontology
updated 3 days ago by
Ram
43k • written 3 days ago by
Sony
▴ 10
0
votes
1
reply
133
views
SNP VCF files from hybrid populations and parental populations generated by GBS in public databases
contaminations
verification
parental
check
updated 1 day ago by
Ram
43k • written 1 day ago by
Hajar
• 0
2
votes
2
replies
127
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
updated 18 hours ago by
dariober
14k • written 23 hours ago by
Pumla
• 0
1
vote
2
replies
126
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 18 hours ago by
Ram
43k • written 22 hours ago by
gdfsnkfns
• 0
0
votes
1
reply
125
views
How can I remove duplicate SNP?
plink
updated 1 day ago by
iraun
6.2k • written 1 day ago by
Zhennan
• 0
0
votes
2
replies
121
views
Error running local blastn in R using system2
blastn
NCBI
R
updated 11 hours ago by
Mensur Dlakic
★ 26k • written 14 hours ago by
Harrison
• 0
0
votes
1
reply
119
views
Normalization strategies for comparing mapped reads across samples in RNA-seq
normalization
rnaseq
updated 19 hours ago by
Ram
43k • written 21 hours ago by
Picasa
▴ 640
0
votes
0
replies
115
views
Visium dataset distance between spots calculations
SpatialSeq
Visium
updated 2 days ago by
GenoMax
140k • written 2 days ago by
houssi301
• 0
1
vote
0
replies
109
views
checkm lineage.ms output file
checkm
lineage
4 days ago by
A_heath
▴ 160
0
votes
0
replies
109
views
Correlation analysis in single-cell sequencing data
scRNA-seq
correlation
scATAC-seq
3 days ago by
Yingying
• 0
3
votes
2
replies
109
views
Gene reads all zero for each sample
R
salmon
DE
DESeq2
18 hours ago by
DYLAN NICO
• 0
0
votes
1
reply
108
views
Wanting to make a Venn diagram of ATACseq peak files, unsure of where to start
ATAC-seq
updated 1 day ago by
Yogi
▴ 70 • written 1 day ago by
Ronin
• 0
0
votes
0
replies
106
views
t2t Reference gtf file
t2t
3 days ago by
Emre
• 0
0
votes
0
replies
105
views
MIENTURNET - miRNA enrichment analysis
miRNA-enrichment
mRNA
RNA
updated 3 days ago by
Ram
43k • written 3 days ago by
PBC
▴ 10
0
votes
0
replies
104
views
How to calculate weighted transcript length for each gene?
salmon
tximport
rna-seq
updated 3 days ago by
Ram
43k • written 3 days ago by
barrypraveen
▴ 130
1
vote
2
replies
104
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP
CPU
transcriptomics
1 hour ago by
Mohamed Abderrahmane
▴ 10
0
votes
0
replies
104
views
bulk RNA-seq: how to remove batch effect between multiple batches and labels?
combat
batch
2 days ago by
kiraqueen
• 0
0
votes
0
replies
103
views
Merging Hi-C datasets originating from experiments using different enzymes
enzymes
Hi-C
updated 2 days ago by
Ram
43k • written 2 days ago by
hamarillo
▴ 70
0
votes
0
replies
103
views
Convert VCF file and add covariate information
VCF
PED
PLINK
2 days ago by
asmariyaz23
▴ 10
0
votes
0
replies
100
views
doing some ontology enrichment analysis
GO
1 day ago by
aleksk779
• 0
0
votes
0
replies
99
views
What is the usual basecalls length and reference mapping length relationship?
genome
alignment
rna-seq
updated 4 days ago by
Carlo Yague
8.6k • written 4 days ago by
anne
• 0
0
votes
1
reply
98
views
(sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
scRNA-seq
updated 20 hours ago by
Ram
43k • written 20 hours ago by
chiditatawmbi
• 0
0
votes
0
replies
98
views
Training
chip-seq
ScATAC-seq
22 hours ago by
Manhezz
• 0
0
votes
0
replies
98
views
Best codeml model for estimating omega, M0 ?
codeml
ete3
evol
2 days ago by
Adrian Pelin
★ 2.6k
1
vote
0
replies
97
views
Downloading immne signature and pathway signature genes form publication and KEGG
genes
TRANSCRIPTOME_signature
3 days ago by
mrazib0210
▴ 10
0
votes
0
replies
97
views
OSCC Dataset downlod using TCGA biolink
R
OSSC
TCGAbiolink
GDC
updated 3 days ago by
Ram
43k • written 4 days ago by
Biogeek
• 0
0
votes
1
reply
97
views
Merging featureCounts output for different species
featureCounts
RNA-seq
updated 16 hours ago by
Ram
43k • written 1 day ago by
Christian
• 0
0
votes
0
replies
93
views
In scRNA, How should I set QC standards?
scRNA
QC
1 day ago by
mnx0723
• 0
0
votes
0
replies
92
views
How to access an image (slice) of interest in spatial analysis
spatial-transcriptomics
Seurat
Visium
updated 2 days ago by
Ram
43k • written 2 days ago by
piotto
▴ 20
0
votes
0
replies
92
views
Variant Enrichment Analysis
Analysis
Enrichment
VEP
Variant
1 day ago by
Mojtaba
• 0
0
votes
1
reply
90
views
vcf file: number of samples does not match number of columns
vcf
bcftools
updated 12 hours ago by
Pierre Lindenbaum
160k • written 13 hours ago by
ekirsch
• 0
0
votes
0
replies
89
views
How to check if a few pathways have relationship?
MSigdb
REACTOME
KEGG
1 day ago by
Chris
▴ 260
0
votes
0
replies
88
views
Multifactor Analysis in DiffBind
DiffBind
ChIPseq
ChIP-seq
3 days ago by
erbrocato
• 0
0
votes
0
replies
86
views
meta-analysis on RNA seq AND microarray results
microarray
RNA
1 day ago by
liuyibin2005
• 0
0
votes
0
replies
85
views
Number of pathway result from GSVA
GSVA
1 day ago by
Chris
▴ 260
0
votes
0
replies
85
views
single cell data integration approach
comparison
integration
pairwise
singlecell
1 day ago by
Jay
• 0
0
votes
0
replies
84
views
Public datasets for genome-wide level mRNA-protein correlation calculation?
mRNA
protein
correlation
4 days ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
84
views
Metacoder plot_cladogram long calculation times
Metacoder
updated 3 days ago by
Ram
43k • written 3 days ago by
La52dA97b6
• 0
0
votes
0
replies
81
views
Association Module to traits
module-trait-relationships
WGCNA
GENIE3
DOMINO
updated 1 day ago by
Ram
43k • written 1 day ago by
r.shiasi3897
▴ 10
0
votes
0
replies
80
views
How to change alternate conformation occupancy ?
Bio.PDB.Atom
Bio.PDB
biopython
updated 19 hours ago by
Ram
43k • written 21 hours ago by
udakshi
• 0
0
votes
0
replies
79
views
GSEA number dimension of expression dataset
GSEA
1 day ago by
edoardofilippi1998
• 0
115 results • Page
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Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of the 'Other' Endocrine Regulatory Systems in Health and Disease", Volume II
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
Comment: Gene reads all zero for each sample
Synthetic lethality and cancer database
Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Comment: Mapping ortholog human and mouse transcript
by
BioinfGuru
★ 1.6k
That error is on the server side, nothing to do with you, and is very common. Usually the fix is to try again in an hour, or to insert host…
Comment: Nanopore multisample variant calling
by
emilydolivo97
• 0
hello @colindaven , Did you find a suitable tool for this purpose please ? I'm dealing with fungal dataset
Comment: How do I get the gene annotations as a text file from a genebank file?
by
BioinfGuru
★ 1.6k
Can you upload or post a link to the genbank file please?
Comment: Mapping ortholog human and mouse transcript
by
manaswwm
▴ 490
I usually perform biomaRt queries with their `getBM()` function where I list the input using `filter` and `values` option and my request in…
Comment: DESeq2 and normalization
by
JH
• 0
Thank you for your response. I have often seen commands like dds <- estimateSizeFactors(dds) normalized_counts <- counts(dds, normalized=T…
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
by
Mohamed Abderrahmane
▴ 10
It's the case that there's no indication of multi-threading in the documentation. However, it made me wonder why the developers would restr…
Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
by
Soheil
▴ 90
Bulk RNAseq from any sample is still considered a bulk sample. Running bulk RNA sequencing on a sample with any level of cell type/state c…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
Comment: Error in openning FastQC
by
GenoMax
140k
At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to…
Comment: vcf file: number of samples does not match number of columns
by
Pierre Lindenbaum
160k
> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
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