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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
8
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP
CPU
transcriptomics
27 minutes ago by
Mohamed Abderrahmane
▴ 10
2
votes
2
replies
16
views
Gene reads all zero for each sample
R
salmon
DE
DESeq2
10 minutes ago by
DYLAN NICO
• 0
0
votes
0
replies
18
views
Contradictions in GSEA results
GSEA
Enrichment-analysis
PEA
updated 1 hour ago by
Ram
43k • written 1 hour ago by
Tolga
▴ 20
0
votes
0
replies
14
views
Illumina Dna Prep kit for sequencing phage linear genomes
tagmentation
transposons
phagetermini
sequencing
1 hour ago by
alenew.am
• 0
0
votes
3
replies
176
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
50 minutes ago by
Nitin
• 0
0
votes
1
reply
29
views
(sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
scRNA-seq
updated 1 hour ago by
Ram
43k • written 2 hours ago by
chiditatawmbi
• 0
0
votes
1
reply
48
views
Normalization strategies for comparing mapped reads across samples in RNA-seq
normalization
rnaseq
updated 1 hour ago by
Ram
43k • written 2 hours ago by
Picasa
▴ 640
0
votes
0
replies
40
views
How to change alternate conformation occupancy ?
Bio.PDB.Atom
Bio.PDB
biopython
updated 40 minutes ago by
Ram
43k • written 3 hours ago by
udakshi
• 0
0
votes
0
replies
51
views
Training
chip-seq
ScATAC-seq
3 hours ago by
Manhezz
• 0
1
vote
10
replies
183
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
20 minutes ago by
Lila M
★ 1.2k
2
votes
2
replies
65
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
updated 9 minutes ago by
dariober
14k • written 5 hours ago by
Pumla
• 0
0
votes
1
reply
65
views
Merging featureCounts output for different species
featureCount
RNAseq
updated 5 hours ago by
andrebolerbarros
• 0 • written 6 hours ago by
Christian
• 0
0
votes
0
replies
45
views
Combine rename and rmdup in SeqKit to remove duplicate sequences and append N in header? Sort by occurence?
seqkit
fasta
6 hours ago by
Broccoli
• 0
0
votes
0
replies
45
views
Is there a good tool/reference for PBP and porin analysis
PBP
porin
6 hours ago by
blur
▴ 280
0
votes
0
replies
53
views
meta-analysis on RNA seq AND microarray results
microarray
RNA
7 hours ago by
liuyibin2005
• 0
0
votes
0
replies
41
views
SPOTlight deconvolution logFC, logFC cohen or mean.AUC
spatial-transcriptomics
SPOTlight
logFC
deconvolution
updated 1 hour ago by
Ram
43k • written 7 hours ago by
M'zelle
• 0
0
votes
0
replies
62
views
In scRNA, How should I set QC standards?
scRNA
QC
10 hours ago by
mnx0723
• 0
0
votes
0
replies
52
views
Annotation of Complex genomes using NCBI Genome Workbench
Genome-Workbench
MAKER
updated 1 hour ago by
Ram
43k • written 11 hours ago by
SAsciences
• 0
0
votes
0
replies
61
views
How to check if a few pathways have relationship?
MSigdb
REACTOME
KEGG
13 hours ago by
Chris
▴ 260
2
votes
10
replies
698
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 1 hour ago by
Ram
43k • written 5 weeks ago by
Sky
▴ 10
0
votes
0
replies
77
views
doing some ontology enrichment analysis
GO
16 hours ago by
aleksk779
• 0
0
votes
2
replies
147
views
novel and know mir156 and mir172
a
updated 16 hours ago by
gayachit
▴ 200 • written 19 hours ago by
Fadmo
• 0
2
votes
8
replies
240
views
Piping samtools to R
R
NGS
bash
samtools
20 hours ago by
joe
▴ 470
0
votes
8
replies
406
views
STAR aligner options
STAR
6 hours ago by
theophile
• 0
0
votes
2
replies
156
views
Why counting by diffbind and featurecounts differ?
featurecounts
diffbind
18 hours ago by
Ankit
▴ 500
0
votes
1
reply
103
views
Wanting to make a Venn diagram of ATACseq peak files, unsure of where to start
ATAC-seq
updated 23 hours ago by
Yogi
▴ 70 • written 1 day ago by
Ronin
• 0
0
votes
0
replies
80
views
Association Module to traits
module-trait-relationships
WGCNA
GENIE3
DOMINO
updated 22 hours ago by
Ram
43k • written 1 day ago by
r.shiasi3897
▴ 10
0
votes
0
replies
80
views
Number of pathway result from GSVA
GSVA
1 day ago by
Chris
▴ 260
0
votes
1
reply
119
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
1
reply
129
views
SNP VCF files from hybrid populations and parental populations generated by GBS in public databases
contaminations
verification
parental
check
updated 22 hours ago by
Ram
43k • written 1 day ago by
Hajar
• 0
0
votes
0
replies
76
views
Creating a custom ontology for peptides
ontology
peptide
1 day ago by
Mathew
• 0
0
votes
0
replies
77
views
GSEA number dimension of expression dataset
GSEA
1 day ago by
edoardofilippi1998
• 0
0
votes
0
replies
84
views
single cell data integration approach
comparison
integration
pairwise
singlecell
1 day ago by
Jay
• 0
0
votes
3
replies
211
views
High number of detected genes per cell after doublet removal - scRNAseq data
scRNAseq
duoblet
1 day ago by
sarahmanderni
▴ 100
0
votes
2
replies
150
views
Error with goodSamplesGenes()
R
WGCNA
23 hours ago by
bioinfo_enthusiast
• 0
0
votes
0
replies
91
views
Variant Enrichment Analysis
Analysis
Enrichment
VEP
Variant
1 day ago by
Mojtaba
• 0
0
votes
7
replies
310
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 17 hours ago by
GenoMax
140k • written 1 day ago by
Patadu94
• 0
0
votes
1
reply
142
views
dbsnp flanks information
dbsnp
updated 1 day ago by
Pierre Lindenbaum
160k • written 1 day ago by
sskimvd
• 0
0
votes
1
reply
137
views
Cell communacations analysis. I only have the proteome of one type of cell
How
to
updated 1 day ago by
ATpoint
81k • written 1 day ago by
David Arturo
• 0
0
votes
0
replies
102
views
bulk RNA-seq: how to remove batch effect between multiple batches and labels?
combat
batch
1 day ago by
kiraqueen
• 0
2
votes
2
replies
207
views
A pipeline for prediction and annotation of obelisks
rna-seq
updated 1 day ago by
Pierre Lindenbaum
160k • written 1 day ago by
fred.s.kremer
▴ 110
0
votes
0
replies
99
views
Convert VCF file and add covariate information
VCF
PED
PLINK
1 day ago by
asmariyaz23
▴ 10
0
votes
0
replies
99
views
Merging Hi-C datasets originating from experiments using different enzymes
enzymes
Hi-C
updated 1 day ago by
Ram
43k • written 1 day ago by
hamarillo
▴ 70
2
votes
3
replies
238
views
Extracting information from my VCF file
VCF
updated 1 day ago by
bioruffo
▴ 40 • written 1 day ago by
realtreeecat
• 0
0
votes
4
replies
239
views
Coverage observed in introns in the Knockdown genes but not in knockout genes
RNA-seq
STAR
IGV
4 hours ago by
rohitsatyam102
▴ 840
0
votes
2
replies
270
views
JASPAR2024_getMatrixSet error
getMatrixSet
JASPAR2024
updated 2 days ago by
Ram
43k • written 5 weeks ago by
maplewj
▴ 10
0
votes
0
replies
91
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
1
reply
162
views
MACS3 or SEACR
MACS3
SEACR
updated 2 days ago by
jared.andrews07
★ 16k • written 2 days ago by
daffodil
▴ 10
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
0
votes
0
replies
97
views
Best codeml model for estimating omega, M0 ?
codeml
ete3
evol
2 days ago by
Adrian Pelin
★ 2.6k
1,000 results • Page
1 of 20
Recent Votes
Comment: Volcano Plot Output Inquiry: Graphs Facing Down
Comment: Gene reads all zero for each sample
Comment: Gene reads all zero for each sample
A: What Is The Sequencing 'Depth' ?
A: Read Duplicates
A: Read Duplicates
How can two contradicted gene sets be enriched in a cancer sample in GSEA analysis?
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104k
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160k
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beacamara
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blur
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81k
Recent Replies
Comment: Volcano Plot Output Inquiry: Graphs Facing Down
by
dariober
14k
Perhaps more concerning is why you have features (genes?) with small pvalue but fold-change very close to zero. It's also unusual that ther…
Comment: Gene reads all zero for each sample
by
DYLAN NICO
• 0
Thank you for the suggestions. Unfortunately I cannot add any details for lack of information. But I will try using a different alignment a…
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
They are +ve and -ve strands, but identical two by two ... I can filter that out later on. This is probably a very naive question, but what…
Comment: Gene reads all zero for each sample
by
ATpoint
81k
Do I understand correctly that you have one gene you are interested in, but all counts are zero, right? If so, first thing could be to use …
Answer: ONT direct RNA sequencing
by
joe
▴ 470
You should use `cat` on .gz files, part of the magic of .gz ...I guess if you use `zcat` they are unzipped and this is why you get the erro…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
thank you !!
Answer: Can I have multiple active GDC download tokens?
by
Zhenyu Zhang
★ 1.1k
You can only have one active token at a time, but you can copy the same token as many times as you want and use them in different computers…
Comment: Parsing fasta file by coordinates
by
sorrymouse
▴ 120
Yes, thats correct. A lot of the responses are addressing problems other than the one I have - I don't want to cluster the sequences based …
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Not sure if I am missing something but you want 4 copies of the same sequence with a different fasta header?
Comment: Normalization strategies for comparing mapped reads across samples in RNA-seq
by
Ram
43k
> TPM seems like a good method, but it may not be suitable here because it requires gene/transcript length. Also because TPM cannot be com…
Comment: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
Nitin
• 0
I did run the `JoinLayers()` even then it is not working, here is the output before and after ```r DefaultAssay(combined1) <- 'RNA' com…
Comment: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
Nitin
• 0
I tried that too. It did not work.
Comment: (sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
by
GenoMax
140k
Try SRA-explorer with search terms you want. Guide here: https://www.biostars.org/p/366721/ Check these portals: https://singlecell.broad…
Comment: Issue with making local BLAST database
by
Begonia_pavonina
▴ 140
Thank you @genomax, if I have well understood the `retmax` parameter and 10000 entries limitation are linked to the R package, and not to t…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
thank you , this is my code : import sys import os import subprocess class FastpFiltering: def __init__(self, input_folder, fastp_ou…
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