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115,819 results • Page
1 of 2317
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34
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Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 7 minutes ago by
aUser
▴ 30 • written 7.5 years ago by
martinguerrerog89
▴ 310
0
votes
1
reply
19
views
Issues With Cram -> Fastq from GTEx v8 WGS
fastq
GTEx
cram
updated 17 minutes ago by
Pierre Lindenbaum
160k • written 33 minutes ago by
Vullnet
• 0
0
votes
2
replies
40
views
DEG (Differential expression gene) analysis
DEG
R
updated 52 minutes ago by
dsull
★ 5.6k • written 1 hour ago by
sooni
▴ 20
0
votes
1
reply
81
views
Biobambam vs Picard in RNA Sequencing Analysis for BAM to FASTQ
RNA-seq
Biobambam
Picard
updated 1 hour ago by
Zhenyu Zhang
★ 1.1k • written 12 hours ago by
kcarey
• 0
791
votes
167
replies
138k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 8 weeks ago by
Biostar
2.5k • written 7.3 years ago by
Istvan Albert
100k
0
votes
0
replies
22
views
News:
Online course: Adaptation Genomics
StructuralVariants
Selection
AdaptationGenomics
PopulationStructure
2 hours ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
23
views
News:
Online course: Analysis of Prokaryotic Pangenomes
BacterialGenomics
Pangenomics
2 hours ago by
carlopecoraro2
★ 2.4k
0
votes
1
reply
58
views
library(scater)
sce
scRNASeq
scater
updated 3 hours ago by
Mensur Dlakic
★ 26k • written 4 hours ago by
Nitin
• 0
0
votes
1
reply
154
views
Is it better to pool samples prior to running deseq2, or should the algorithm be run separately for every pool?
deseq2
RNA-seq
updated 5 hours ago by
swbarnes2
14k • written 8 hours ago by
Shelby
• 0
0
votes
4
replies
214
views
Expert Guidance Required for De Novo Transcriptome Analysis
Transcriptome
De-novo
updated 6 hours ago by
Doomhammer
• 0 • written 20 hours ago by
ben@f
▴ 10
0
votes
1
reply
488
views
Downloading epigenetic and mutation data of specific TCGA BRCA samples
Mutation
RNA-Seq
TCGA
updated 7 hours ago by
aUser
▴ 30 • written 2.6 years ago by
Soura
• 0
0
votes
1
reply
100
views
Beagle Phasing and Imputation
imputation
phasing
beagle
updated 10 hours ago by
LChart
3.8k • written 13 hours ago by
Duarte Molha
▴ 240
0
votes
1
reply
89
views
Subsetting Seurat object based on list of cell barcodes
seurat
updated 5 hours ago by
Ming Tommy Tang
★ 3.8k • written 10 hours ago by
bgbs
• 0
4
votes
4
replies
201
views
Differential express genes in imbalance groups
Limma
7 hours ago by
Chris
▴ 260
2
votes
1
reply
102
views
basal gene expression level
RNA-Seq
updated 12 hours ago by
LChart
3.8k • written 12 hours ago by
Francois Piumi
▴ 40
0
votes
0
replies
60
views
Evaluating MAST model fit using AIC
cell
single
MAST
scRNA
transcriptomics
12 hours ago by
mhale
• 0
0
votes
1
reply
112
views
Seurat 5 integration
integration
seurat
updated 13 hours ago by
jared.andrews07
★ 16k • written 15 hours ago by
sarahmanderni
▴ 100
0
votes
3
replies
150
views
scRNAseq normalization
scRNA-seq
SCT
updated 5 hours ago by
Ming Tommy Tang
★ 3.8k • written 13 hours ago by
sarahmanderni
▴ 100
3
votes
7
replies
1.2k
views
7 follow
Transcription Start Site
TSS
updated 5 hours ago by
Ming Tommy Tang
★ 3.8k • written 23 months ago by
Fatemeh Nabizadeh
▴ 10
0
votes
0
replies
67
views
Limma contrasts - difference between single and multiple concurrent contrasts results
R
limma
updated 14 hours ago by
Ram
43k • written 14 hours ago by
shasabhi1
• 0
0
votes
0
replies
69
views
Genotype simulation
gwas
simulation
sim1000
updated 15 hours ago by
Ram
43k • written 16 hours ago by
Eliza
▴ 30
0
votes
0
replies
58
views
Tabula Sapiens and scanpy normalised expression data
scanpy
scRNA-seq
10x
normalisation
updated 15 hours ago by
Ram
43k • written 16 hours ago by
matt.a.bennett25890
• 0
4
votes
2
replies
133
views
Problem with .bed file
cygwin64
bed
PLINK
updated 12 hours ago by
Ram
43k • written 16 hours ago by
Dinmukhamed
• 0
0
votes
1
reply
174
views
compareCluster's enrichGO difference in results when stating ont = "ALL" vs NULL
enrichGO
clusterProfiler
updated 17 hours ago by
Dunois
★ 2.5k • written 1 day ago by
TIANTHING JESTLIN
• 0
0
votes
0
replies
72
views
Remove SNPs based on MAF in Fst analysis
SNP
MAF
Fst
Popgenome
17 hours ago by
kopelol
▴ 20
4
votes
2
replies
222
views
Before or after LD clumping for PRS calculation in GWAS
GWAS
2 hours ago by
경준
▴ 20
1
vote
2
replies
236
views
Trim Galore: Automatic detection of adapters
trimgalore
12 hours ago by
Daniel
▴ 30
0
votes
0
replies
77
views
Troubleshooting a REGENIE sex-stratified GWAS
GWAS
REGENIE
19 hours ago by
s.may-wilson
▴ 40
0
votes
3
replies
187
views
Average expression of a sample in single-cell data
single-cell
rna-seq
updated 5 hours ago by
dsull
★ 5.6k • written 19 hours ago by
newuser2024
• 0
0
votes
4
replies
229
views
blastn: 2.2.31+ Package: blast 2.2.31, build Jun 2 2015 10:47:46
blastn
blast
ubuntu
updated 15 hours ago by
SequenceServer
▴ 140 • written 22 hours ago by
Luca
• 0
0
votes
2
replies
151
views
nf-core/rnaseq, problem with ensembl reference
nfcore
nextflow
ensembl
rnaseq
16 hours ago by
Filip
• 0
0
votes
1
reply
107
views
Haddock 2.4
Protein
Docking
updated 21 hours ago by
dthorbur
★ 1.6k • written 22 hours ago by
Preeti
• 0
0
votes
1
reply
122
views
Deeptools scale issue for plotHeatmap
deeptools
computeMatrix
plotHeatmap
updated 16 hours ago by
Ram
43k • written 22 hours ago by
Learner
• 0
1
vote
1
reply
106
views
turning old shell ncbi querys into url querys
eutils
ncbi
updated 21 hours ago by
GenoMax
140k • written 22 hours ago by
Guelakais
• 0
0
votes
1
reply
452
views
ArchR Doublet Inference to Signac
Signac
scATAC-seq
ArchR
updated 22 hours ago by
fracarb8
★ 1.5k • written 13 months ago by
bioinformatics.girl
▴ 20
0
votes
2
replies
154
views
calculating mean fragment length from CollectInsertSizeMetrics(Picard) output
count2fpkm
20 hours ago by
Niharika
• 0
3
votes
10
replies
622
views
t-test in two groups, multiple rows
R
t-test
8 hours ago by
sooni
▴ 20
3
votes
4
replies
1.3k
views
sam.gz files to bam using samtools
RNA-Seq
samtools
updated 1 day ago by
robertoalbanese.bioinfo
• 0 • written 12 months ago by
tikshyadav19
• 0
0
votes
3
replies
163
views
error in wigToBigWig while converting mappability to bedgraph
mappability
gem
bedgraph
wigToBigWig
updated 40 minutes ago by
Pierre Lindenbaum
160k • written 1 day ago by
Dora
▴ 10
0
votes
0
replies
98
views
Forum:
Field of Study in Computational Biology
Genomics
Computational-Biology
PhD
updated 16 hours ago by
Ram
43k • written 1 day ago by
Mohammed
• 0
0
votes
2
replies
164
views
FASTA/FASTQ files of fetal Aneuploids
nipt
21 hours ago by
lolbye_1
• 0
0
votes
0
replies
108
views
comparing sc-seq combination and bulk-sequencing
bulk-sequencing
sc-sequencing
1 day ago by
润达
• 0
1
vote
1
reply
195
views
Finding homologous protein sequence using blastp led to the same sequence as output
Blastp
updated 1 day ago by
Mensur Dlakic
★ 26k • written 1 day ago by
hamid sta
▴ 10
1
vote
1
reply
150
views
Where to download DOCK 6.11?
docking
updated 1 day ago by
ATpoint
81k • written 1 day ago by
tsakeliz
• 0
0
votes
1
reply
143
views
BRIG coverage.graph issues
BRIG
sam
updated 1 day ago by
Pierre Lindenbaum
160k • written 1 day ago by
dlera.lozano
• 0
0
votes
0
replies
114
views
How to generate a comparative map using CGview?
genome
map
CGView
1 day ago by
marongiu.luigi
▴ 710
0
votes
0
replies
128
views
Advice on telling if two SNPs are on the same haplotype
ldpair
halplotype
co-occurance
gnomad
snp
1 day ago by
amy__
▴ 160
2
votes
1
reply
239
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
Clinical
TCGA-BRCA
TCGAbiolinks
Treatment-response
TCGA
updated 2 days ago by
Zhenyu Zhang
★ 1.1k • written 6 days ago by
vibhamishra017
▴ 10
1
vote
2
replies
402
views
RNA-seq differential expression across multiple tissues, 2 trials, and 2 conditions
RNA-seq
DESeq
EdgeR
Batch-effect
DEGs
23 hours ago by
BioinfGuru
★ 1.6k
1
vote
1
reply
212
views
Compute p-value, having log fold change
p-value
fold-change
updated 16 hours ago by
Ram
43k • written 2 days ago by
Ngrin
• 0
115,819 results • Page
1 of 2317
Recent Votes
A: Using A Variable As A Blocking Factor Vs Putting It As A Term In The Model Formu
Answer: Before or after LD clumping for PRS calculation in GWAS
Comment: CAZy database has multiple family sequence...
RNA-seq differential expression across multiple tissues, 2 trials, and 2 conditions
Answer: Differential express genes in imbalance groups
Answer: Differential express genes in imbalance groups
Comment: Differential express genes in imbalance groups
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Recent Replies
Answer: TCGA UUIDS to TCGA barcode (SampleID) in R
by
aUser
▴ 30
Great solutions on this page, the old web page has been replace with new one, so you need to use the new link, and it will work: old lin…
Comment: Issues With Cram -> Fastq from GTEx v8 WGS
by
Pierre Lindenbaum
160k
unless your cram in sorted on query rather than on coordinate, your cram must be first sort processed with collate: https://twitter.com/lh…
Comment: error in wigToBigWig while converting mappability to bedgraph
by
Pierre Lindenbaum
160k
remove the spaces from your "chrom" key variableStep chrom=NT_173277 span=5 or may be quote the chrom variableStep chrom="NT_173277.1 C…
Comment: DEG (Differential expression gene) analysis
by
dsull
★ 5.6k
Well, I guess expression could be measured from the DNA indirectly such as with RNA Pol II binding to DNA via ChIP-seq but then the OP shou…
Answer: DEG (Differential expression gene) analysis
by
dsull
★ 5.6k
What exactly is "DNA-level DEG"? That makes zero sense. DEG = Differential **EXPRESSION** of genes. In any case, for RNA sequencing data, …
Answer: Biobambam vs Picard in RNA Sequencing Analysis for BAM to FASTQ
by
Zhenyu Zhang
★ 1.1k
Let me say even if you had used the exactly same bioinformatics steps, you will still have batch efforts from sample collection, storage an…
Comment: Before or after LD clumping for PRS calculation in GWAS
by
경준
▴ 20
1. I think i misunderstood logistic regression of association test. Now I understand. 2. you're right. Thank you for your helpful reply sam…
Comment: library(scater)
by
Mensur Dlakic
★ 26k
> I am not able to install the package scater as per the webpage I urge you to read back what you wrote and think whether you'd be able to…
Comment: How to corrected test statistics based on the LDSC intercept?
by
Isaac
• 0
Thank you very much!
Comment: Transcription Start Site
by
Ming Tommy Tang
★ 3.8k
you can use bioconductor as shown in this post using Genomicanges https://support.bioconductor.org/p/46508/
Comment: scRNAseq normalization
by
Ming Tommy Tang
★ 3.8k
To be honest, I really do not use SCT, and use log normalization all the time...
Comment: Subsetting Seurat object based on list of cell barcodes
by
Ming Tommy Tang
★ 3.8k
index<- rownames(seurat.obj_combined) %in% all_good_cells_rhemac10$V1 seurat.obj_combined[index, ] should do the trick
Comment: Average expression of a sample in single-cell data
by
dsull
★ 5.6k
Well, if you're only sequencing the very end (the 3' end) of transcripts, how are you going to detect any of the splice junctions that appe…
Answer: Is it better to pool samples prior to running deseq2, or should the algorithm be
by
swbarnes2
14k
> Seems like pooling all should be statistically more robust. Yup. So put everything into the same DESeq2 object. See: https://…
Answer: Expert Guidance Required for De Novo Transcriptome Analysis
by
Doomhammer
• 0
Do you have enough clean data to assemble, for each genotypes independently? I think at first we should find the difference in transcripts …
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