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14,232 results • Page
2 of 285
Sort: Rank
Rank
Views
Votes
Replies
2
votes
10
replies
730
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 21 hours ago by
Ram
43k • written 5 weeks ago by
Sky
▴ 10
3
votes
2
replies
293
views
FDR and Bonferroni
FDR
Bonferroni
updated 1 day ago by
joe
▴ 470 • written 3 days ago by
song
• 0
0
votes
1
reply
496
views
Which fasta files are assembled transcripts IDBA_tran assembler ?
RNA-Seq
Assembly
updated 1 day ago by
weidonglu
• 0 • written 3.8 years ago by
sunnykevin97
▴ 980
0
votes
0
replies
100
views
doing some ontology enrichment analysis
GO
1 day ago by
aleksk779
• 0
2
votes
1
reply
196
views
Choosing an FC Threshold
statistics
rna-seq
updated 1 day ago by
Gordon Smyth
★ 6.9k • written 2 days ago by
Netanel
• 0
0
votes
1
reply
132
views
Converting AutoDock-Vina PDBQTs to PDB files
Docking
AutoDock
Vina
PDBQT
PDB
updated 1 day ago by
Mensur Dlakic
★ 26k • written 1 day ago by
Ricard
• 0
0
votes
2
replies
164
views
novel and know mir156 and mir172
a
updated 1 day ago by
gayachit
▴ 200 • written 1 day ago by
Fadmo
• 0
0
votes
1
reply
108
views
Update R in Posit Workbench
R
Posit
updated 1 day ago by
Ram
43k • written 1 day ago by
Nitin
• 0
2
votes
8
replies
263
views
Piping samtools to R
R
NGS
bash
samtools
1 day ago by
joe
▴ 470
8
votes
6
replies
406
views
Pangenome of plant
pangenome
plant
updated 1 day ago by
talbots
• 0 • written 2 days ago by
analyst
▴ 10
1
vote
2
replies
188
views
vg call is time consuming
vg
1 day ago by
Maxine
▴ 40
4
votes
14
replies
4.5k
views
8 follow
Installation: Tax4Fun2 package are not found and github repository is not maintained anymore
Tax4Fun2
updated 1 day ago by
Ram
43k • written 21 months ago by
Elsa
▴ 20
0
votes
8
replies
420
views
STAR aligner options
STAR
1 day ago by
theophile
• 0
2
votes
3
replies
512
views
Website or tool to obtain a list of genes that participate in a specific process?
genomics
updated 1 day ago by
NancyTLi
• 0 • written 3 months ago by
Hamtaro
▴ 50
0
votes
2
replies
299
views
How to obtain Node/ Edge information from a Reactome Pathway
R
API
pathways
reactome
databases
updated 1 day ago by
GenoMax
140k • written 4 weeks ago by
K.patel5
▴ 140
0
votes
2
replies
167
views
Why counting by diffbind and featurecounts differ?
featurecounts
diffbind
1 day ago by
Ankit
▴ 500
0
votes
1
reply
109
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
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
85
views
Number of pathway result from GSVA
GSVA
1 day ago by
Chris
▴ 260
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
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
0
votes
0
replies
78
views
Creating a custom ontology for peptides
ontology
peptide
1 day ago by
Mathew
• 0
0
votes
3
replies
223
views
convert cds to seurat object
R
monocle3
seurat
updated 1 day ago by
edoardofilippi1998
• 0 • written 2 days ago by
sooni
▴ 20
0
votes
0
replies
79
views
GSEA number dimension of expression dataset
GSEA
1 day ago by
edoardofilippi1998
• 0
0
votes
2
replies
217
views
Limma compare between 3 conditions vs 2 conditions
Limma
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
3
replies
218
views
High number of detected genes per cell after doublet removal - scRNAseq data
scRNAseq
duoblet
1 day ago by
sarahmanderni
▴ 100
1
vote
2
replies
222
views
DESeq2 and normalization
RNA-seq
normalization
DESeq2
2 hours ago by
JH
• 0
0
votes
2
replies
155
views
Error with goodSamplesGenes()
R
WGCNA
1 day ago by
bioinfo_enthusiast
• 0
0
votes
0
replies
94
views
Variant Enrichment Analysis
Analysis
Enrichment
VEP
Variant
2 days ago by
Mojtaba
• 0
0
votes
7
replies
324
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 1 day ago by
GenoMax
140k • written 2 days ago by
Patadu94
• 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
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
104
views
bulk RNA-seq: how to remove batch effect between multiple batches and labels?
combat
batch
2 days ago by
kiraqueen
• 0
2
votes
2
replies
216
views
A pipeline for prediction and annotation of obelisks
rna-seq
updated 1 day ago by
Pierre Lindenbaum
160k • written 2 days ago by
fred.s.kremer
▴ 110
6
votes
12
replies
5.5k
views
6 follow
Getting sample information from GEO
GEO
NCBI
updated 2 days ago by
Tania
• 0 • written 6.9 years ago by
Tom_L
▴ 350
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
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
2
replies
218
views
Using the Ontology Lookup Service (OLS) API
API
OLS
1 day ago by
longoka
▴ 40
7
votes
2
replies
203
views
Create a new reference genome with denovo assembly and standard reference with long read data?
PacBio
updated 2 days ago by
gconcepcion
▴ 410 • written 2 days ago by
eorr
▴ 30
2
votes
3
replies
242
views
Extracting information from my VCF file
VCF
updated 2 days ago by
bioruffo
▴ 40 • written 2 days ago by
realtreeecat
• 0
0
votes
4
replies
246
views
Coverage observed in introns in the Knockdown genes but not in knockout genes
RNA-seq
STAR
IGV
1 day ago by
rohitsatyam102
▴ 840
0
votes
2
replies
271
views
JASPAR2024_getMatrixSet error
getMatrixSet
JASPAR2024
updated 2 days ago by
Ram
43k • written 5 weeks ago by
maplewj
▴ 10
2
votes
3
replies
479
views
Should I use Dfam or a custom repetitve elements library (from PlantRep) as a repeat database; using RepeatMasker in a Linux machine?
genome
sequence
repeatmasker
blast
updated 2 days ago by
b.contreras.moreira
▴ 70 • written 3 days ago by
Vijith
▴ 30
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
2
replies
185
views
Fpkm and log2fold change and pcr validation
fpkm
updated 2 days ago by
bioruffo
▴ 40 • written 2 days ago by
mounavisirekolam
• 0
2
votes
2
replies
204
views
Location of NCBI ftp site changed?
ftp
ncbi
2 days ago by
sampsa.hyvamaki
• 0
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
98
views
Best codeml model for estimating omega, M0 ?
codeml
ete3
evol
2 days ago by
Adrian Pelin
★ 2.6k
14,232 results • Page
2 of 285
Recent Votes
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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▴ 460
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Comment: Mapping ortholog human and mouse transcript
by
1769mkc
★ 1.2k
for hgnc and ensembl that can be done for transcript id for human to mouse ortholog its difficult to parse and map the exact version from g…
Comment: Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of
by
Mensur Dlakic
★ 26k
Take it from someone who has hosted both a successful and a failed research topic: these deadlines are unrealistic. I am guessing you are p…
Answer: Tissue specific mRNA expression dataset in human and mouse
by
BioinfGuru
★ 1.6k
Awesome, years ago I wrote my thesis on the use of Tau to calculate tissue specificity, enjoy! The supplementary materials in the paper is…
Answer: 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…
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