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121,937 results • Page 135 of 2439
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2
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8
replies
1.4k
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Expert Guidance Required for De Novo Transcriptome Analysis
Transcriptome De-novo
updated 18 months ago by 154k • written 18 months ago by ▴ 20
0
votes
1
reply
1.0k
views
Downloading epigenetic and mutation data of specific TCGA BRCA samples
Mutation RNA-Seq TCGA
updated 18 months ago by ▴ 80 • written 4.2 years ago by • 0
4
votes
5
replies
1.6k
views
Differential express genes in imbalance groups
Limma
18 months ago by Chris ▴ 360
3
votes
1
reply
682
views
basal gene expression level
RNA-Seq
updated 18 months ago by 5.1k • written 18 months ago by ▴ 70
0
votes
0
replies
461
views
Evaluating MAST model fit using AIC
cell single MAST scRNA transcriptomics
18 months ago by mhale ▴ 40
1
vote
1
reply
696
views
Seurat 5 integration
integration seurat
updated 18 months ago by ★ 19k • written 18 months ago by ▴ 130
4
votes
5
replies
1.3k
views
scRNAseq normalization
scRNA-seq SCT
updated 18 months ago by 89k • written 18 months ago by ▴ 130
3
votes
7
replies
2.5k
views
7 follow
Transcription Start Site
TSS
updated 18 months ago by ★ 4.7k • written 3.4 years ago by ▴ 10
0
votes
0
replies
454
views
Limma contrasts - difference between single and multiple concurrent contrasts results
R limma
updated 18 months ago by 45k • written 18 months ago by • 0
0
votes
0
replies
392
views
Genotype simulation
gwas simulation sim1000
updated 18 months ago by 45k • written 18 months ago by ▴ 30
5
votes
2
replies
859
views
Problem with .bed file
cygwin64 bed PLINK
updated 18 months ago by 45k • written 18 months ago by ▴ 10
1
vote
1
reply
1.0k
views
compareCluster's enrichGO difference in results when stating ont = "ALL" vs NULL
enrichGO clusterProfiler
updated 18 months ago by ★ 2.9k • written 18 months ago by • 0
0
votes
0
replies
446
views
Remove SNPs based on MAF in Fst analysis
SNP MAF Fst Popgenome
18 months ago by kopelol ▴ 20
4
votes
2
replies
801
views
Before or after LD clumping for PRS calculation in GWAS
GWAS
18 months ago by K Lee ▴ 20
1
vote
2
replies
1.3k
views
Trim Galore: Automatic detection of adapters
trimgalore
18 months ago by Daniel ▴ 30
4
votes
3
replies
1.1k
views
Troubleshooting a REGENIE sex-stratified GWAS
GWAS REGENIE
updated 5 months ago by ▴ 660 • written 18 months ago by ▴ 60
4
votes
4
replies
1.0k
views
Average expression of a sample in single-cell data
single-cell rna-seq
18 months ago by newuser2024 • 0
0
votes
6
replies
1.5k
views
blastn: 2.2.31+ Package: blast 2.2.31, build Jun 2 2015 10:47:46
blastn blast ubuntu
updated 18 months ago by ▴ 150 • written 18 months ago by • 0
1
vote
1
reply
476
views
turning old shell ncbi querys into url querys
eutils ncbi
updated 18 months ago by 154k • written 18 months ago by • 0
0
votes
1
reply
1.1k
views
ArchR Doublet Inference to Signac
Signac scATAC-seq ArchR
updated 18 months ago by ★ 1.7k • written 2.6 years ago by ▴ 30
3
votes
10
replies
2.2k
views
t-test in two groups, multiple rows
R t-test
18 months ago by sooni ▴ 20
3
votes
4
replies
3.1k
views
sam.gz files to bam using samtools
RNA-Seq samtools
updated 18 months ago by • 0 • written 2.6 years ago by • 0
0
votes
4
replies
933
views
error in wigToBigWig while converting mappability to bedgraph
mappability gem bedgraph wigToBigWig
18 months ago by Dora ▴ 10
0
votes
0
replies
534
views
Forum: Field of Study in Computational Biology
Genomics Computational-Biology PhD
updated 18 months ago by 45k • written 18 months ago by • 0
0
votes
2
replies
545
views
FASTA/FASTQ files of fetal Aneuploids
nipt
18 months ago by lolbye_1 • 0
0
votes
0
replies
270
views
comparing sc-seq combination and bulk-sequencing
bulk-sequencing sc-sequencing
18 months ago by 润达 • 0
1
vote
1
reply
597
views
Finding homologous protein sequence using blastp led to the same sequence as output
Blastp
updated 18 months ago by ★ 30k • written 18 months ago by ▴ 10
1
vote
1
reply
593
views
Where to download DOCK 6.11?
docking
updated 18 months ago by 89k • written 18 months ago by • 0
0
votes
1
reply
511
views
BRIG coverage.graph issues
BRIG sam
updated 18 months ago by 166k • written 18 months ago by ▴ 10
0
votes
0
replies
481
views
How to generate a comparative map using CGview?
genome map CGView
18 months ago by marongiu.luigi ▴ 760
0
votes
0
replies
487
views
Advice on telling if two SNPs are on the same haplotype
ldpair halplotype co-occurance gnomad snp
18 months ago by amy__ ▴ 250
2
votes
1
reply
808
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
Clinical TCGA-BRCA TCGAbiolinks Treatment-response TCGA
updated 18 months ago by ★ 1.3k • written 18 months ago by ▴ 10
1
vote
2
replies
921
views
RNA-seq differential expression across multiple tissues, 2 trials, and 2 conditions
RNA-seq DESeq EdgeR Batch-effect DEGs
18 months ago by BioinfGuru ★ 2.1k
2
votes
1
reply
708
views
Compute p-value, having log fold change
p-value fold-change
updated 18 months ago by 45k • written 18 months ago by • 0
1
vote
2
replies
1.8k
views
(ERR): "GRCh38_noalt_as" does not exist or is not a Bowtie 2 index Exiting now ...
alignment genomics bowtie bowtie2
updated 18 months ago by 45k • written 19 months ago by • 0
1
vote
2
replies
724
views
Upset plot
upsetplot
18 months ago by Chris ▴ 360
0
votes
1
reply
562
views
Are there any tools for mutational analysis of viruses?
virus
updated 18 months ago by 45k • written 18 months ago by ▴ 10
0
votes
6
replies
2.0k
views
How to corrected test statistics based on the LDSC intercept?
LDSC intercept
18 months ago by Isaac • 0
0
votes
2
replies
876
views
I can't add VAF from population for all of my variants from VCF file
vaf vcf genomics gnomad allelicfrequency
18 months ago by Samuel ▴ 20
0
votes
0
replies
391
views
Analyzing differentially methylated regions from Nanopore long read data?
Long-read-sequencing methylation
updated 18 months ago by 45k • written 18 months ago by ▴ 20
2
votes
2
replies
939
views
Seeking help with Tcga Target Gtex Expected Count Data
R TCGA gTEX
18 months ago by bioinfo_enthusiast • 0
1
vote
1
reply
760
views
Issues with "chanw0/MRS" R package and dependencies
ANCOMBC densvis chanw0MRS scater
18 months ago by emi-smiley ▴ 10
1
vote
0
replies
448
views
How should I regenotype VCFs using vg?
vg
18 months ago by Ricky ▴ 10
1
vote
2
replies
753
views
What GC content should I expect?
RNA-seq GC-content
updated 18 months ago by 89k • written 18 months ago by ★ 2.1k
0
votes
0
replies
282
views
stat test
stattest chi2
updated 18 months ago by 154k • written 18 months ago by • 0
2
votes
6
replies
1.6k
views
How to look up gene names using SNP locations on Practical Haplotype Graph
rphg phg
updated 16 months ago by ▴ 420 • written 18 months ago by • 0
0
votes
0
replies
480
views
Anvio HMM source campbell_et_al
anvio
updated 18 months ago by 45k • written 18 months ago by ▴ 40
0
votes
1
reply
835
views
Reactome Species Comparison - analysis table
reactome
updated 18 months ago by ▴ 20 • written 2.5 years ago by ▴ 120
0
votes
1
reply
1.1k
views
Fold change vs signal p-value in ENCODE ATAC-seq
encode bigwig atac-seq
updated 18 months ago by 5.1k • written 18 months ago by • 0
0
votes
1
reply
694
views
Issue with bigWigSummary utility of Kent/UCSC utilities
bigWig UCSC
updated 18 months ago by 166k • written 18 months ago by • 0
121,937 results • Page 135 of 2439
Recent Votes
A: How to normalize my rna seq data?
Answer: Linear regression vs DESeq2 models for DEG analysis
Answer: Linear regression vs DESeq2 models for DEG analysis
Answer: Linear regression vs DESeq2 models for DEG analysis
Answer: Linear regression vs DESeq2 models for DEG analysis
Answer: Linear regression vs DESeq2 models for DEG analysis
Answer: Linear regression vs DESeq2 models for DEG analysis
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Recent Replies
Comment: Linear regression vs DESeq2 models for DEG analysis by ATpoint 89k
+1 Our answer should be the top-voted answer in this thread https://www.biostars.org/p/284775/ as it actually addresses conceptual differ…
Comment: Linear regression vs DESeq2 models for DEG analysis by swbarnes2 15k
It is not clear to me that you can meaningfully correct for 5 different batches with two samples a piece.
Comment: Does this adapter content from fastqc to warrant trimming prior to alignment? by GenoMax 154k
> I am not sure if there would be primer dimer sequences I should have said adapter dimers above. Correction made.
Comment: Help understanding this per base sequence content failure fastqc plot by lieven.sterck 15k
that 151st base added is a base to ignore (it's a kind of random addition) ... if I recall correctly it's a consequence of the technology. …
Comment: Linear regression vs DESeq2 models for DEG analysis by FioG • 0
@swbarnes2 Thank you for your response! I am new to RNA seq analysis and was originally recommended to use the LM method following cqn and …
Comment: Does this adapter content from fastqc to warrant trimming prior to alignment? by curious ▴ 890
Thank you, the adapter sequences are specified as CTGTCTCTTATACACATCT+ATGTGTATAAGAGACA is the SampleSheet.csv file from the sequencing run.…
Comment: how to explain the sample size discrepancy in UCSC Xena by nuorain ▴ 40
Thank you very much.
Answer: how to explain the sample size discrepancy in UCSC Xena by i.sudbery 22k
Because there wasn't RNA-seq analysis performed for every sample in TCGA?
Answer: Linear regression vs DESeq2 models for DEG analysis by i.sudbery 22k
There are two main problems with using linear models for read-count based analyses. Firstly, linear models assume a normal distribution…
Comment: real time PCR data analysis by ATpoint 89k
I cannot guide on GraphPad. It's commercial software so better contact their support.
Answer: Linear regression vs DESeq2 models for DEG analysis by swbarnes2 15k
DE genes in bulk RNASeq is what DESeq2 was made for, so why wouldn't you use it? RPKM is not an appropriate normalization method here. M…
Comment: What happened to biomart.org by Jeremy Leipzig 23k
same with geuvadis.org
Comment: real time PCR data analysis by Gordon Smyth ★ 8.3k
Are you doing qPCR for one gene or for several genes?
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…
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