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121,931 results • Page
100 of 2439
Sort: Rank
Rank
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Votes
Replies
1
vote
1
reply
772
views
TensorQTL Mapping - permutation p values for all associations
permutation
TensorQTL
15 months ago by
Paula
▴ 10
1
vote
3
replies
829
views
How to do preprocessing from fastqc
fastqc
scRNA-seq
single-cell
updated 15 months ago by
Ram
45k • written 15 months ago by
Lulu
• 0
4
votes
2
replies
871
views
Trying to use equivalence test from a diffbind dataset
Diffbind
R
DESeq2
ChIP-seq
ATAC-seq
updated 15 months ago by
ATpoint
89k • written 15 months ago by
jandrade
▴ 20
2
votes
2
replies
1.2k
views
Consistent cluster coloring
R
Seurat
15 months ago by
solo.albif
• 0
1
vote
3
replies
2.0k
views
Slot to pull data from for DoHeatmap
DESeq2
DoHeatmap
Seurat
Pseudobulk
updated 15 months ago by
Ming Tommy Tang
★ 4.7k • written 15 months ago by
bio_info
▴ 20
0
votes
0
replies
513
views
News:
online course on Adaptation Genomics
Structural-Variants
Population-Genomics
Adaptation-Genomics
updated 15 months ago by
Ram
45k • written 15 months ago by
Physalia-courses
★ 2.6k
2
votes
3
replies
2.5k
views
Is it possible to modify the gene names from the x-axis in Seurat::Dotplot?
seurat
scRNA-seq
single-cell
dotplot
updated 15 months ago by
Ram
45k • written 15 months ago by
ev97
▴ 40
0
votes
0
replies
506
views
Setting the size for finding motifs using homer
motif
homer
15 months ago by
gogeni5529
▴ 80
12
votes
13
replies
8.4k
views
7 follow
Centrimo error: Template does not contain data section
ChIP-Seq
MEME
updated 15 months ago by
Johan Zicola
▴ 80 • written 6.0 years ago by
Matus
▴ 70
2
votes
2
replies
835
views
Finding DEGs of cell type comprising of more than one clusters
DEG
FindAllMarkers
scRNA-seq
single-cell
updated 15 months ago by
Ram
45k • written 15 months ago by
TNF_alpha
• 0
0
votes
0
replies
391
views
Clustering a rare variant on the GDA array
array
gda
clustering
rare-variant
genome-studio
updated 15 months ago by
Ram
45k • written 15 months ago by
panacotaforcota
• 0
4
votes
3
replies
1.3k
views
PCR duplicate removal in single-end atac-seq data
ATAC-seq
pcr-duplicate
updated 15 months ago by
ATpoint
89k • written 15 months ago by
sarahmanderni
▴ 130
0
votes
6
replies
1.6k
views
METAL ERROR: The command you issued could not be processed ...
meta-analysis
METAL
GWAS
11 months ago by
JJ
• 0
2
votes
1
reply
841
views
dbSNP download and merge to my data
SNP
GWAS
dbSNP
updated 15 months ago by
GenoMax
154k • written 15 months ago by
SeoG
▴ 10
4
votes
2
replies
1.0k
views
NGS Data Analysis
NGS
Genome
sequencing
updated 15 months ago by
a.alnawfal.1992
▴ 360 • written 15 months ago by
Bindiya
▴ 10
0
votes
1
reply
800
views
Annotating Pathways in a network
Pathways
Cytoscape
Network
updated 15 months ago by
Scooter
▴ 310 • written 15 months ago by
SKY
▴ 60
0
votes
2
replies
836
views
Enrichment Analysis of Pathways
Enrichment-Analysis
cytoscape
updated 15 months ago by
Scooter
▴ 310 • written 15 months ago by
SKY
▴ 60
3
votes
7
replies
2.3k
views
Salmon ~ Effective Length
Salmon
updated 15 months ago by
Rob
7.1k • written 16 months ago by
chrisk
• 0
2
votes
5
replies
1.8k
views
MAKER2 no FASTAs generated
MAKER
FASTA
fasta_merge
genome annotation
updated 15 months ago by
Kinoppy
• 0 • written 5.4 years ago by
jamie.pike
▴ 90
0
votes
1
reply
584
views
vg giraffe, accept admixed single and paired reads as input
vg
updated 15 months ago by
Jordan M Eizenga
▴ 760 • written 15 months ago by
Thomas
• 0
0
votes
0
replies
348
views
vg search for all specific kmer/motif (e.g., RE site) occurrences in pangenome graph
vg
15 months ago by
Thomas
• 0
2
votes
2
replies
970
views
Phasing human samples with Shapeit4
Phasing
Shapeit
Shapeit4
15 months ago by
Private
▴ 10
0
votes
4
replies
953
views
In silico PCR - multiple Primers and multiple sequences at the same time
pcr
updated 14 months ago by
Ram
45k • written 15 months ago by
sulichkarolina
• 0
1
vote
2
replies
691
views
scaling for kallisto estimate counts
Differential-gene-expression
RNAlysis
Kallisto
15 months ago by
Meghan.T
▴ 10
2
votes
3
replies
2.0k
views
Submitting to GEO: 10x Fixed RNA profiling (Single Cell Gene Expression Flex)
rna-seq
updated 15 months ago by
matthewsmith
▴ 10 • written 15 months ago by
psm
▴ 170
0
votes
0
replies
1.0k
views
Tutorial:
DiffBind run parallel
CHIP-seq
ATAC-seq
DiffBind
updated 15 months ago by
ATpoint
89k • written 15 months ago by
Juan
• 0
1
vote
1
reply
905
views
MGI DNBelab C Series High-throughput Single-cell RNA Library Preparation Set V3.0, Seurat
rna-seq
seurat
single-cell
mgi
updated 15 months ago by
bk11
★ 3.1k • written 15 months ago by
yau
• 0
1
vote
7
replies
1.7k
views
Looking for clarification of .vcf output from variant calling
freebayes
vcf
variant-calling
updated 15 months ago by
Ram
45k • written 15 months ago by
Jess
▴ 60
0
votes
0
replies
471
views
KEGG pathways analysis (ko and map IDs)
ko
kegg
pathway
map
updated 15 months ago by
GenoMax
154k • written 15 months ago by
manekineko
▴ 10
0
votes
4
replies
1.1k
views
circlize R package to plot ecDNA
ecDNA
plot
circlize
updated 12 months ago by
trausch
★ 2.0k • written 15 months ago by
a.loka92
• 0
0
votes
2
replies
655
views
Determining biological relevance of a list of motifs?
motifs
HOMER
15 months ago by
Ronin
▴ 10
0
votes
4
replies
1.2k
views
Is using the assembled transcript in one de novo assembler as reference/trusted contigs for the second assembler logical?
Trinity
RNA-seq
rnaSPAdes
updated 15 months ago by
GenoMax
154k • written 15 months ago by
RCMC
• 0
6
votes
6
replies
1.8k
views
Best way to create a custom reference for CellRanger when using a transgenic mouse strain expressing a human protein.
cellranger
updated 15 months ago by
ATpoint
89k • written 15 months ago by
Alx
• 0
0
votes
0
replies
349
views
RMSD vs SDM (structural distance)
RMSD
15 months ago by
Coralie
• 0
1
vote
2
replies
750
views
cluster annotation in single-cell (-nuclei) RNA-Seq or multiome experiments
celldex
annotation
singler
scRNAseq
clustering
15 months ago by
gogeni5529
▴ 80
0
votes
2
replies
1.1k
views
Speed of Cell-Cell interaction analysis on scRNA-seq data
Cellchat
scRNA-seq
Seurat
updated 15 months ago by
gglim
▴ 220 • written 2.3 years ago by
Song
▴ 10
0
votes
0
replies
349
views
Overrepresentation analysis for fractions
overrepresentation
15 months ago by
malonzm1
▴ 20
1
vote
1
reply
2.0k
views
Uniprot SPARQL: InterPro domain positions
sparql
updated 15 months ago by
me
▴ 760 • written 7.4 years ago by
fabian.grammes
▴ 10
1
vote
12
replies
2.7k
views
6 follow
blast Segmentation fault
blastn
fasta
local-blast
updated 15 months ago by
Ram
45k • written 19 months ago by
giulia.cosenza
▴ 20
0
votes
2
replies
1.4k
views
Ubuntu 24.04 for Oxford Nanopore Mk1B
Ubuntu
installation
Software
15 months ago by
Calvin-Calvin
• 0
3
votes
5
replies
902
views
sam2tsv add in my path
sam2tsv
updated 15 months ago by
Pierre Lindenbaum
166k • written 15 months ago by
harry
▴ 40
5
votes
3
replies
926
views
FastQC report
quality
fastqc
filtration
updated 15 months ago by
a.alnawfal.1992
▴ 360 • written 15 months ago by
analyst
▴ 70
0
votes
6
replies
1.3k
views
Stuck on how to run STARsolo on paired cDNA RNA-Seq FASTQ files
STARsolo
FASTQ
15 months ago by
Nicholas
▴ 20
0
votes
0
replies
380
views
PCa Biplot For RNA-Seq Study Samples With 1k Genome Reference Panel
ethnicity
snp
hapmap
15 months ago by
ssankar3
• 0
1
vote
7
replies
11k
views
7 follow
Using bcftools to change ploidy level in vcf files
snp
bcftools
updated 15 months ago by
michael
▴ 20 • written 8.4 years ago by
flolil27
• 0
0
votes
0
replies
507
views
What is the reason for the requirement of at least 2 experiments for LFQ in MaxQuant?
MaxQuant
Spectrometry
Mass
Proteomics
LFQ
15 months ago by
Riq
▴ 50
3
votes
1
reply
594
views
Regarding WGCNA
WGCNA
updated 15 months ago by
Ram
45k • written 15 months ago by
deepak
• 0
0
votes
6
replies
1.4k
views
Why am I getting such a big difference in alignment rates in kallisto?
kallisto
ensembl
15 months ago by
bioinfo
▴ 160
1
vote
1
reply
1.9k
views
Reading files from different types as H5AD
python
scanpy
anndata
single-cell
updated 15 months ago by
bk11
★ 3.1k • written 15 months ago by
AlexStar
▴ 200
1
vote
5
replies
2.8k
views
Error in converting bed file to interval using Picard
WES
exome
BedToIntervalList
picard
agilent
updated 15 months ago by
Ram
45k • written 5.8 years ago by
Assa Yeroslaviz
★ 1.9k
121,931 results • Page
100 of 2439
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Understanding terms, specifically relating to GT:PL in a VCF file
Comment: Looking to learn practical bioinformatics
Answer: WGCNA package in R: dendogram plot error
Answer: Does this adapter content from fastqc to warrant trimming prior to alignment?
Answer: Does this adapter content from fastqc to warrant trimming prior to alignment?
Looking to learn practical bioinformatics
Looking to learn practical bioinformatics
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Recent Replies
Comment: protein interaction prediction
by
Fatemeh
▴ 50
Thanks very much for your help. I need to try it.
Comment: real time PCR data analysis
by
Fatemeh
▴ 50
Thanks a lot for the link. The problem is that with this repeated measures, if you put the data from different donors in different rows, fo…
Answer: What happened to biomart.org
by
GenoMax
154k
Looks like EBI let the domain registration expire. The domain was picked up by someone else and turned into the site OP mentions. There use…
Comment: Hifiasm is getting killed while trying to assemble a genome
by
GenoMax
154k
> I want to reconstruct the assembly using the pacbio reads only. Is there a paper associated with this data? If the original publication/…
Comment: real time PCR data analysis
by
ATpoint
89k
I think the keyword to go after here is repeated measures https://www.graphpad.com/guides/prism/latest/statistics/repeated_measures.htm
Answer: What happened to biomart.org
by
ATpoint
89k
Maybe I am missing sth because I've never used the website but only the API and R interface, but I think the website has always been https:…
Comment: protein interaction prediction
by
Fatemeh
▴ 50
It is most probably binding to a protein. Its function is somehow known though, which is good . Thanks very much for the link. I will have …
Comment: Looking to learn practical bioinformatics
by
Upesh
▴ 20
ATpoint, you are absolutely bang on. In fact, my intention is not to switch careers but to connect with this field and build tools/systems …
Comment: Hifiasm is getting killed while trying to assemble a genome
by
pranavdatar01
• 0
I am trying to reproduce the assembly from the raw pacbio reads. I want to reconstruct the assembly using the pacbio reads only.
Comment: Does this adapter content from fastqc to warrant trimming prior to alignment?
by
ATpoint
89k
I would trim it. Two percent is not much but with WGS, say you have 400mio reads per sample or so, it's still millions of reads that theore…
Comment: Looking to learn practical bioinformatics
by
ATpoint
89k
> How do I connect the dots to a grand vision of drug discovery, DNA analysis, disease etc. Despite that computational-driven data analys…
Comment: Looking to learn practical bioinformatics
by
Upesh
▴ 20
Thank you, genomax, for the recommendations! Very helpful!
Comment: Learning Biology/Bioinformatic Basics
by
Upesh
▴ 20
For anyone landing on this page, the updated link is: [https://www.langmead-lab.org/teaching.html][1] [1]: https://www.langmead-lab.org/…
Comment: Looking to learn practical bioinformatics
by
GenoMax
154k
This (or a variation) question is asked every so often. You may want to take a look at these past threads and the discussions in there to g…
Answer: Does this adapter content from fastqc to warrant trimming prior to alignment?
by
GenoMax
154k
It is an investment in time and will ensure that there is no extraneous sequence is present, if you choose to do scanning/trimming. That …
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