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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
53
views
ONT Live-Basecalling Issue?
ONT
minKNOW
live-basecalling
7 hours ago by
Akshay
• 0
0
votes
0
replies
44
views
cell signaling networks: which are the options to Ingenuity?
R
ingenuity
biological
networks
3 hours ago by
pinheirofabiano
▴ 100
0
votes
0
replies
55
views
Identify gene from sequence at scale in non-model organisms
name
sequence
gene
11 hours ago by
matthewmerkin32
• 0
0
votes
0
replies
98
views
Seeking Advice on Causal Inference for Treatment Effect Prediction (Small Sample, Genomic Covariates)
inference
causal
17 hours ago by
oghzzang
▴ 50
0
votes
0
replies
64
views
How to save the AlphaFold PAE plot as an image in ChimeraX using command line ?
PAE
ChimeraX
AlphaFold
17 hours ago by
Picasa
▴ 670
0
votes
1
reply
132
views
Blastx issue
Long
coding
non
blastx
RNA
updated 22 hours ago by
JustinZhang
▴ 130 • written 1 day ago by
Avik
• 0
1
vote
10
replies
394
views
How to test the similarity of two gene expression profiles
test
gene
sets
updated 23 hours ago by
JustinZhang
▴ 130 • written 2 days ago by
htchd
• 0
0
votes
0
replies
83
views
Error using DWLS
deconvolution
DWLS
RNAseq
1 day ago by
Ana
• 0
0
votes
5
replies
1.6k
views
How to remove this module selection error?
WGCNA
updated 1 day ago by
香
• 0 • written 2.3 years ago by
gupta00aritra
• 0
0
votes
1
reply
450
views
bbsplit : How to configure ambiguous/ambiguous2 parameters in order to consider as unmapped reads, reads mapped on both human/mouse references.
bbsplit
nextflow
updated 1 day ago by
GenoMax
150k • written 1 day ago by
ZheFrench
▴ 590
1
vote
2
replies
140
views
Limma for DEG aalysis
R
DEG
limma
ANALYSIS
1 day ago by
rahma.khoualdia
• 0
0
votes
0
replies
109
views
deletion impact
vcf
updated 1 day ago by
GenoMax
150k • written 1 day ago by
HarperReed
• 0
0
votes
2
replies
154
views
Help finding GTEx v8 file
GTEx
SHAPEIT2
22 hours ago by
蒲蒲
• 0
2
votes
5
replies
207
views
Idat file processing issue with command line cli
CanineHTS
IDAT
1 day ago by
1769mkc
★ 1.2k
0
votes
0
replies
90
views
What is the best way to know if a pair of genes is random?
terms
genes
go
1 day ago by
Ana
• 0
0
votes
0
replies
87
views
is there a way to get --ref paths to prioritize my order with vg call?
call
vgcall
1 day ago by
PolenP
• 0
0
votes
0
replies
108
views
filtering genes before or after the correlation?
co-expression
feature
selection
correlation
2 days ago by
tyasird
▴ 10
1
vote
2
replies
190
views
Is Centering and Scaling Essential for Expression Data as Input for Machine Learning Algorithms?
featureselection
microarray
preprocessing
2 days ago by
Sib
▴ 60
0
votes
0
replies
139
views
Demultiplexing samples when barcodes repeat: Any advice?
seurat
demultiplex
singlecell
scRNAseq
3 days ago by
tia
• 0
0
votes
2
replies
213
views
Steps for meta-analysis
Meta-Analysis
differential-expression
updated 2 days ago by
Ram
45k • written 3 days ago by
majorprogeria
• 0
0
votes
0
replies
164
views
how pd tag were defined in gaf file
vg
3 days ago by
chuanj8848
• 0
0
votes
0
replies
135
views
Using DEXseq on kallisto tsv outputs ?
alignement
DEXseq
kallisto
3 days ago by
Gerard
▴ 10
0
votes
0
replies
149
views
GTDB-tk classify_wf
GTDB-tk
classification
taxonomic
3 days ago by
pranjalarun10
• 0
0
votes
1
reply
513
views
Help finding proteases that most likely cleaved a peptide from a full-length protein
R
peptides
proteasix
updated 3 days ago by
Fatemeh
▴ 40 • written 18 months ago by
georgiamorgannn
• 0
0
votes
0
replies
140
views
protease candidates for my protein of interest
cleaving-site
proteases
protein
3 days ago by
Fatemeh
▴ 40
0
votes
0
replies
149
views
Need Help Regarding Back-Splicing Junction Coordinates in CIRI2 Output
circRNA
CIRI2
updated 4 days ago by
GenoMax
150k • written 4 days ago by
Faraz
• 0
1
vote
1
reply
208
views
Short reads to identify stuctural variants
SV
long-read
short-read
updated 3 days ago by
Istvan Albert
102k • written 4 days ago by
priya.bmg
▴ 70
0
votes
0
replies
325
views
Best approach for SNP calling in tumor single-cell multiome data (scRNA-seq + scATAC-seq) for CNV analysis
variant
SNP
single-cell
4 days ago by
nilaylale88
• 0
0
votes
3
replies
274
views
C.reinhardtii single-cell Seurat object - gene names instead of loci
loci
Chlamydomonas
single-cell
updated 4 days ago by
GenoMax
150k • written 4 days ago by
Ana
• 0
0
votes
3
replies
238
views
Snakemake Global Environment Container
Snakemake
Conda
Singularity
updated 3 days ago by
DBScan
▴ 470 • written 4 days ago by
meetmet
• 0
0
votes
2
replies
234
views
GTF repeatmasker annotation file
repeatmasker
GTF
updated 3 days ago by
rfran010
★ 1.4k • written 4 days ago by
frarodmar17
• 0
0
votes
1
reply
175
views
How to select GEO datasets for differential expression analysis using GEO2R
GEO
DEGs
GEO2R
updated 4 days ago by
ATpoint
87k • written 4 days ago by
dreamer247
• 0
0
votes
4
replies
765
views
PopGenome lost individual information
PopGenome
updated 4 days ago by
Arup Ghosh
3.3k • written 12 months ago by
Yixuan
• 0
1
vote
5
replies
309
views
Polishing raw nanopore reads with Pacbio
polishing
assembly
4 days ago by
samuel.a.odonnell
▴ 590
0
votes
1
reply
224
views
Why does Radian run so much slower than vanilla R?
R
Python
Radian
VS-Code
updated 4 days ago by
Istvan Albert
102k • written 5 days ago by
RR
• 0
0
votes
0
replies
139
views
Significant SNPs with the same effect in FarmCPU
effect-size
gwas
FarmCPU
likage-disequilibrium
5 days ago by
AndrMod
• 0
0
votes
0
replies
143
views
rrvgo::getGoSize error
ReViGO
GO-terms
rrvgo
updated 5 days ago by
Ram
45k • written 5 days ago by
Ana
• 0
0
votes
0
replies
139
views
Genotype Imputation for VCF File via API Using R ?
Genotype-Imputation
VCF
API
5 days ago by
Ahmed Jaber
• 0
0
votes
0
replies
155
views
How label Group list after integratin scRNA-seq and scATAC-seq data
ArchR
5 days ago by
Bioinformatics_16
• 0
0
votes
7
replies
529
views
Error in importing data from 10x genomics into RStudio
H5
file
scRNA
RStudio
5 days ago by
himanshu0102
• 0
1
vote
2
replies
255
views
WGS for CNV and Aneuploidy analysis
CNV
Aneuploidy
WGS
4 days ago by
bioinfo1990
▴ 10
0
votes
1
reply
562
views
Issues with T2T in pigeon prepare from isoseq
long-read
isoseq
rna-seq
updated 5 days ago by
Ram
45k • written 6 months ago by
SethJ
• 0
0
votes
2
replies
311
views
how to do a corellation analysis of multiple CRISPR data sets
crispr-screen
batch-effect
correlation
updated 5 days ago by
Ram
45k • written 8 days ago by
Assa Yeroslaviz
★ 1.9k
0
votes
1
reply
272
views
How to put distinct colors to connection bridges in the Sankey plot ?
R
Python
Sankey
updated 8 days ago by
zx8754
12k • written 9 days ago by
ohtang7
▴ 40
1
vote
1
reply
282
views
PCA comparison of cell line vs tumors
RNAseq
Sequencing
PCA
Normalization
updated 5 days ago by
ATpoint
87k • written 9 days ago by
karlensberg
• 0
0
votes
0
replies
203
views
Need help defining a threshold
DAVID
Genes
GO
9 days ago by
Ana
• 0
0
votes
0
replies
215
views
How can I use mcmcglmm to calculate whether two traits are correlated?
glmm
statistics
evolution
10 days ago by
雨
▴ 20
1
vote
8
replies
1.7k
views
6 follow
FastQC on nanopore data: high proportion of polyA and polyG. Why ?
fastQC
polyG
ONT
nanopore
polyA
updated 9 days ago by
lieven.sterck
15k • written 13 months ago by
Matt
• 0
0
votes
6
replies
543
views
miRNA-seq normalization
miRDeep2
normalization
RNA-seq
miRNA-seq
miRNA
7 days ago by
paulanavarrete116
• 0
0
votes
2
replies
347
views
DEG analysys using pseudobulk from single cell RNA-seq
DEG
scRNA-seq
10 days ago by
Diego
▴ 110
1,000 results • Page
1 of 20
Recent Votes
Insert Size And Fragment Size ?
A: Insert Size And Fragment Size ?
A: Insert Size And Fragment Size ?
Insert Size And Fragment Size ?
A: Big differences with CollectHsMetrics
A: Big differences with CollectHsMetrics
Answer: Picard gives empty value for HS_LIBRARY_SIZE when running CollectHsMetrics
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Recent Replies
Comment: TPM vs FPKM divergence at high values
by
pinheirofabiano
▴ 100
I don't have a better mathematical explanation, but FPKMs are not reliable for gene expression studies, there are many discussions about t…
Comment: TPM vs FPKM divergence at high values
by
megancgrdnr
• 0
Thank you for your answer! Do you have any sense of why the expression values diverge at higher-expressed genes? I can't see anything in th…
Comment: What does vg autoindex mpmap do?
by
Jordan M Eizenga
▴ 690
GCSA indexing certainly can be time consuming. On a reasonably well-behaved graph (such as those derived from VCFs, or usually those from t…
Comment: WGCNA
by
1769mkc
★ 1.2k
what your gene expression matrix size or dimension?
Answer: WGCNA
by
PFSXR
• 0
There are too few valid genes in the input matrix expr_filtered, possibly because after the goodSamplesGenes filtering, only the grey modul…
Comment: Batch effect
by
Picasa
▴ 670
~ batch + condition
Answer: Batch effect
by
pinheirofabiano
▴ 100
please read this paper: [ComBat-seq][1] [1]: https://academic.oup.com/nargab/article/2/3/lqaa078/5909519
Answer: convert Gene ID to Gene Symbol
by
pinheirofabiano
▴ 100
I asked the same question months ago... [https://www.biostars.org/p/9604385/][1] [1]: https://www.biostars.org/p/9604385/
Answer: TPM vs FPKM divergence at high values
by
pinheirofabiano
▴ 100
Go with TPM, when you use TPM, the sum of all TPMs in each sample are the same. This makes it easier to compare the proportion of reads tha…
Comment: Help finding GTEx v8 file
by
蒲蒲
• 0
Thank you for your reply, but when I tried to log in to ANVIL, I was told that I didn't have access, so I tried to ask for help.
Comment: Blastx issue
by
JustinZhang
▴ 130
Check this out: [Biorixv][1] [1]: https://www.biorxiv.org/content/10.1101/2024.08.18.608522v1.full
Comment: How to test the similarity of two gene expression profiles
by
JustinZhang
▴ 130
Is it hard for you to list the number of samples and runs? If you cannot figure it out, at least you can show the number of files and their…
Comment: How to test the similarity of two gene expression profiles
by
JustinZhang
▴ 130
Then just upload the csv/tsv to LLMs.
Comment: How to keep the same view for different AlphaFold 3 simulations in ChimeraX?
by
LauferVA
4.7k
would you mind posting this as a separate question, then linking to this question and @ me?
Comment: How to test the similarity of two gene expression profiles
by
htchd
• 0
Sorry, I thought they are the same. I have two gene expression profiles(each with one column of gene name, and another column of fold chang…
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