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1,015 results • Page
2 of 21
Sort: Votes
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Views
Votes
Replies
8
votes
6
replies
2.5k
views
Batch effect removal with the help of sva
SVA
batch-effect
gene-expression
updated 26 days ago by
Ram
43k • written 3.5 years ago by
Gene_MMP8
▴ 240
8
votes
8
replies
676
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 10 days ago by
swbarnes2
14k • written 11 days ago by
Aaliya
▴ 10
8
votes
4
replies
3.0k
views
Read count correlation between samples
differential-gene-expression
RNA-seq
updated 25 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
8
votes
5
replies
5.8k
views
ISCN annotation for SV/CN VCF files
SV
written 8 months ago by
a.beggs
▴ 60
8
votes
6
replies
2.6k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 17 days ago by
John Marshall
3.0k • written 2.0 years ago by
bioguy24
▴ 230
8
votes
16
replies
1.0k
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 8 days ago by
bk11
★ 2.4k • written 8 weeks ago by
Sofia
• 0
8
votes
2
replies
812
views
News:
FINAL CALL - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (May 6-8, 2024 in Berlin)
single-cell
sequencing
29 days ago by
David Langenberger
11k
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression
TPM
RNA-Seq
counts
batch-effect
17 days ago by
Ram
43k
7
votes
8
replies
689
views
Why are the basics so complicated? Basic coverage filtering for VCF files
filter
vcf
coverage
updated 22 days ago by
spen
▴ 40 • written 25 days ago by
MBarcelo
▴ 40
7
votes
3
replies
4.6k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA
RNA-Seq
batch-effect
updated 17 days ago by
Ram
43k • written 5.1 years ago by
tujuchuanli
▴ 100
7
votes
6
replies
541
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
13 days ago by
analyst
▴ 30
7
votes
2
replies
3.7k
views
Timeout on getBM() to retrieve snps from locations
biomaRt
getBM
R
updated 18 days ago by
Ram
43k • written 5.2 years ago by
Corentin
▴ 600
7
votes
3
replies
1.2k
views
biomaRt::getSequence - Invalid type argument
biomaRt
R
updated 18 days ago by
Ram
43k • written 3.9 years ago by
mbk0asis
▴ 690
7
votes
7
replies
599
views
Can you suggest a protein PDB that has two chainst but only 50 total number of atoms?
protein
pdb
protein-databank
updated 22 days ago by
Matthias Zepper
4.6k • written 22 days ago by
4fzcgueyp5
• 0
7
votes
6
replies
1.3k
views
using different microarray datasets (meta-analysis?) for DEG pipeline
microarray
meta-analysis
DEG
batch-effect
updated 17 days ago by
Ram
43k • written 4.9 years ago by
mosesoo
▴ 30
7
votes
20
replies
6.5k
views
7 follow
Repeat masked gtf files from ensembl
ensembl
RNA-Seq
genome
updated 23 days ago by
e.r.zakiev
▴ 210 • written 4.3 years ago by
kevin.stachelek
▴ 80
7
votes
4
replies
2.1k
views
filtering genes by pearson correlation
correlation
RNA-Seq
R
updated 18 days ago by
Ram
43k • written 6.1 years ago by
mannoulag1
▴ 120
7
votes
2
replies
300
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 11 days ago by
geneontologyhelp
▴ 390 • written 12 days ago by
catherine.teyssier
• 0
7
votes
10
replies
2.7k
views
6 follow
Batch effect correction to compare differentially expressed genes across datasets
batch
batch-effect
DESeq2
rna-seq
updated 18 days ago by
Ram
43k • written 2.0 years ago by
mmitra
▴ 60
7
votes
16
replies
734
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
6 days ago by
Ruqaiya
• 0
7
votes
7
replies
1.1k
views
Prediction tools summary - zero values
statistics
updated 18 days ago by
Дана
• 0 • written 6 months ago by
Lukas
▴ 50
7
votes
3
replies
2.9k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 16 days ago by
colindaven
6.4k • written 16 months ago by
Dr.Animo
▴ 130
7
votes
4
replies
1.4k
views
Is there any journal article to reference removeBatchEffect function from Limma?
batch
removebatcheffect
limma
rna-seq
batch-effect
updated 18 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 9 days ago by
rohitsatyam102
▴ 850 • written 6.1 years ago by
smallfish
▴ 10
7
votes
7
replies
1.5k
views
Forum:
Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career
advice
updated 19 days ago by
Dunois
★ 2.5k • written 20 days ago by
AdviceSeeker
• 0
6
votes
2
replies
1.5k
views
Writing a batch script for analyzing RNA-Seq data
RNA-Seq
quantification
alignment
updated 18 days ago by
Ram
43k • written 5.2 years ago by
mohammedtoufiq91
▴ 250
6
votes
11
replies
3.4k
views
Collapsing probesets to genes on WGCNA
WGCNA
gene-expression
R
updated 18 days ago by
Ram
43k • written 5.3 years ago by
Davide Chicco
▴ 120
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads
illumina
genome-assembly
updated 29 days ago by
Ram
43k • written 2.6 years ago by
predeus
★ 2.0k
6
votes
0
replies
2.6k
views
Tool:
Immuno-Navigator, a batch-corrected database for gene coexpression in the immune system
gene-co-expression
batch-effect
immunology
updated 16 days ago by
Ram
43k • written 7.0 years ago by
alexis.vandenbon
▴ 80
6
votes
4
replies
2.2k
views
Is there a way to get RNAFold output for multifasta in tabular format?
RNAFold
updated 17 days ago by
jakobjung
• 0 • written 4.6 years ago by
adhirajnath14
▴ 40
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 17 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
6
votes
4
replies
1.5k
views
RNA-Seq: X samples and X batches
RNA-Seq
edgeR
DESeq2
Batch-Effect
updated 18 days ago by
Ram
43k • written 5.2 years ago by
Behram Radmanesh
▴ 40
6
votes
10
replies
2.3k
views
Why different DEGs between my result and the author's result?
limma
microarray
differential-gene-expression
updated 25 days ago by
Ram
43k • written 6.1 years ago by
fernardo
▴ 170
6
votes
8
replies
609
views
BRAKER3 genome annotation
annotation
BRAKER3
genome
updated 18 days ago by
dariober
14k • written 20 days ago by
manaswiniparija3
▴ 40
6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna
RNA-Seq
ChIP-Seq
updated 26 days ago by
mflab
• 0 • written 3.9 years ago by
m.sadman.sakib
▴ 120
6
votes
17
replies
6.6k
views
Can you add a label key to heatscatter plot in R?
heatscatter
visualization
R
updated 18 days ago by
Ram
43k • written 9.6 years ago by
james.lloyd
▴ 100
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat
RNA-Seq
Limma
DESeq2
batch-effect
updated 16 days ago by
Ram
43k • written 5.0 years ago by
borkk
▴ 140
6
votes
0
replies
208
views
Herald:
The Biostar Herald for Monday, April 15, 2024
herald
19 days ago by
Biostar
2.7k
6
votes
3
replies
205
views
Interpretting IGV output
IGV
updated 13 days ago by
Carlo Yague
8.7k • written 13 days ago by
analyst
▴ 30
6
votes
6
replies
4.4k
views
10x to cloupe
single-cell-transcriptomics
10x
25 days ago by
firestar
★ 1.6k
5
votes
3
replies
734
views
Illumina reads preprocessing best practice for snp calling applications
Illumina
snp
updated 15 days ago by
Enrique
• 0 • written 9 months ago by
Denis
▴ 310
5
votes
4
replies
683
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
11 days ago by
kirillkirilenko
▴ 40
5
votes
2
replies
1.8k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq
batch
batch-effect
sequencing
updated 18 days ago by
Ram
43k • written 3.0 years ago by
Mat
▴ 60
5
votes
4
replies
371
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
2 days ago by
Estevão
• 0
5
votes
3
replies
410
views
Ensembl assembly choice for DNA reference with no combined primary assembly
alignment
HISAT2
RNA-Seq
ensembl
Assembly
updated 23 days ago by
GenoMax
142k • written 23 days ago by
AHerik
▴ 20
5
votes
13
replies
9.2k
views
8 follow
biomaRt: Timeout on getBM().
r
biomart
ensembl
updated 23 days ago by
Mike Smith
★ 2.0k • written 2.8 years ago by
lincaijin1994
▴ 40
5
votes
4
replies
2.8k
views
genefu for PAM50 prediction
RNA-Seq
breast cancer
subtyping
updated 18 days ago by
hamarillo
▴ 70 • written 5.7 years ago by
silviajserrano
▴ 50
5
votes
6
replies
7.3k
views
scatter plot, aov()
aov
scatter-plot
anova
updated 18 days ago by
Ram
43k • written 3.2 years ago by
Rob
▴ 170
5
votes
5
replies
565
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 1 day ago by
Mbofire
• 0 • written 10 days ago by
Ming Tommy Tang
★ 3.9k
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq
bulk-RNASeq
RNA-Seq
single-cell
updated 24 days ago by
veldahan86
• 0 • written 3.8 years ago by
Assa Yeroslaviz
★ 1.8k
1,015 results • Page
2 of 21
Recent Votes
Comment: Raw counts using stringtie
Comment: Raw counts using stringtie
Answer: GRCh38.gmap file
Comment: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: Design matrix Differential expression analysis
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Comment: The GDC Legacy Archive is retiring soon.
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If you are talking about methylation idat files, they were all migrated from legacy to the data portal. If you are talking about other pl…
Comment: How to access TCGA samples that were treated with a specific drug?
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These TCGA samples were taken 10 ~ 20 years ago, and there is no way they have been treated by the modern immunotherapy. Are you sure tha…
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> When is it recommended to use the design <- cbind(Intercept=1,Group=c(-1,-1,-1,1,1,1)) It is not recommended. No such code appears anywh…
Comment: GRCh38.gmap file
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Hi Mathew, The .txt files provided in the link differ from the .gmap files, but after several attempts, I succeeded in generating the .gma…
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Hi, I have spent some time searching for a GRCH38 map file for you. I have found a certain publication that uses a hg38 genetic map file…
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Hi, You asked three questions so I will attempt to help the best I can **What should be the optimal GC score cutoff** It sounds li…
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Thank you for your explanation. I am working on the cell lines and I am investigating the effect of the treatment on the expression level, …
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I ran into same issue of "duplicated gene symbol(s)": 1: In CIBERSORTxFractions(sigmatrix = sigmatrix, mixture = mixture, : 22292 dup…
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Thank you for your response. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are ind…
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ATpoint
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Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write dow…
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Ruqaiya
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This the tool still problematic?
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Ruqaiya
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Thank you for the advice, i'll keep that in mind.
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Ruqaiya
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I am trying to reproduce some bioinformatics data from a research paper-[this paper][1] as i was asked to work on an MRSA bioinfo project, …
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Mensur Dlakic
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Most likely you didn't do anything wrong. Going by your previous post that you have only 8 GB of RAM, the most likely reason is the lack of…
Comment: Segmentation error while using a tool
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Thanujay S
• 0
Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
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