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156 results • Page
2 of 4
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
125
views
How to summarize dbCAN3 results
dbCAN
CAZy
CAZyme
dbCAN3
dbCAN2
3 days ago by
Nishat
• 0
0
votes
0
replies
137
views
what exactly is a k-mer table (remora)?
remora
basecall
3 days ago by
anne
• 0
1
vote
1
reply
159
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 3 days ago by
dsull
★ 5.8k • written 3 days ago by
niruf
• 0
0
votes
0
replies
127
views
GWAS Phenotypes
GWAS
3 days ago by
solomoncharles77
▴ 90
0
votes
2
replies
288
views
GSEA analysis in R
GSEA
R
Arabidopsis
2 days ago by
Sudip
• 0
0
votes
0
replies
112
views
Add geno header to VariantAnnotation objects
nichenet
scRNA-seq
3 days ago by
QX
• 0
2
votes
5
replies
365
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
3 days ago by
Bikram Kumar
• 0
0
votes
2
replies
233
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 3 days ago by
Ram
43k • written 4 days ago by
David
• 0
1
vote
2
replies
241
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
3 days ago by
bioinfo
▴ 150
0
votes
1
reply
175
views
How to get the reference panel sites for TOPMed hg37 and 38
Imputation
updated 4 days ago by
bk11
★ 2.3k • written 4 days ago by
sinhas
• 0
0
votes
1
reply
191
views
merging Seurat objects after SCT
Seurat
SCT
updated 4 days ago by
Ram
43k • written 4 days ago by
michelle.swarovski
• 0
0
votes
1
reply
172
views
Two databases: Human Microbiome Project and MGnify
Microbiome
databases
updated 4 days ago by
GenoMax
141k • written 4 days ago by
haiying.kong
▴ 360
0
votes
2
replies
243
views
RNAseq 1 control 2 different treatment
RNA-seq
3 days ago by
matteo.levorato
• 0
1
vote
0
replies
132
views
Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
Gene-ontology
RNA-seq
R
updated 4 days ago by
Ram
43k • written 4 days ago by
Oscar
▴ 10
0
votes
0
replies
136
views
How should I make kallisto indexes?
kallisto
updated 4 days ago by
GenoMax
141k • written 4 days ago by
bioinfo
▴ 150
2
votes
0
replies
191
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
4 days ago by
Alexander
▴ 220
1
vote
1
reply
163
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 4 days ago by
GenoMax
141k • written 4 days ago by
eesiribloom
▴ 80
0
votes
0
replies
129
views
Automated internal stop codon checker
ORF
stopcodon
internal
virus
4 days ago by
Balazs Horvath
▴ 10
0
votes
0
replies
131
views
Repeat expansion identification tools for long-read data
fragilex
repeatexpansion
long-read
fmr1
4 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
143
views
FreeBayes detection capacity
reads
freebayes
long
5 days ago by
quentinperriere
• 0
0
votes
2
replies
215
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
2 days ago by
DKA
▴ 40
0
votes
2
replies
238
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
4 days ago by
rj.rezwan
• 0
0
votes
0
replies
155
views
Plotting heatmap of genes in each samples scRNA in Seurat
scRNA
heatmap
5 days ago by
Hien
• 0
0
votes
2
replies
265
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
3 days ago by
Koketso
• 0
0
votes
0
replies
180
views
Novel cyclic peptide structure prediction
protein
structure-prediction
alphafold
peptide
updated 5 days ago by
Ram
43k • written 5 days ago by
menyawino
• 0
1
vote
3
replies
316
views
Ensembl gene id conversion
biomart
ensembl
updated 3 days ago by
ATpoint
81k • written 6 days ago by
naveedhasan2000
• 0
1
vote
2
replies
293
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 4 days ago by
Istvan Albert
100k • written 6 days ago by
Jiang
• 0
0
votes
0
replies
178
views
Core SNP tree VS. concatenated core genome tree
phylogenetic
tree
SNP
6 days ago by
YiweiZhu
▴ 30
0
votes
0
replies
189
views
Somatic and Germline variant calling for tumor, normal and blood sample
germline
variants
somatic
updated 6 days ago by
Ram
43k • written 7 days ago by
anitharavichandran2211
• 0
0
votes
2
replies
306
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
6 days ago by
O.rka
▴ 710
0
votes
6
replies
518
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
4 days ago by
Dunois
★ 2.5k
4
votes
7
replies
527
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 6 days ago by
Ram
43k • written 7 days ago by
AHerik
▴ 20
4
votes
13
replies
787
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 3 days ago by
BioinfGuru
★ 1.7k • written 8 days ago by
matteo.levorato
• 0
1
vote
4
replies
374
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics
htseq-count
RNA-Seq
NGS
hisat2
updated 6 days ago by
BioinfGuru
★ 1.7k • written 8 days ago by
Morteza
• 0
2
votes
2
replies
246
views
How to row normalize a matrixplot?
scRNA-seq
RNA-seq
single-cell
scanpy
4 days ago by
bioinfo
▴ 150
8
votes
10
replies
669
views
bash script
whole-genome-sequencing
updated 4 days ago by
Ram
43k • written 11 days ago by
bestone
▴ 30
0
votes
4
replies
322
views
Compute bootstrap values on consensus tree
phylogeny
tree
raxml
4 days ago by
pablo
▴ 300
1
vote
1
reply
187
views
ComplexHeatmap anno_mark position changes with height of gene expression heatmap
ComplexHeatmap
5 days ago by
CTLong
▴ 110
1
vote
2
replies
265
views
Tumour purity and ploidy estimation
Copy-number
Whole-exome-sequencing
3 days ago by
bp22
▴ 80
0
votes
2
replies
524
views
autodockvina
python
python3
autodock
updated 1 day ago by
Ram
43k • written 3 months ago by
iamsmor
• 0
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray
combat
batch-effect
median-normalization
updated 1 day ago by
Ram
43k • written 18 months ago by
Dominique
• 0
2
votes
6
replies
850
views
Batch effect correction with cell type enrichment analysis
limma
RNA-seq
r
batch-effect
updated 3 days ago by
Ram
43k • written 18 months ago by
JACKY
▴ 140
0
votes
5
replies
2.0k
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq
batch-effect
normalization
updated 3 days ago by
Ram
43k • written 20 months ago by
mmitra
▴ 60
1
vote
2
replies
804
views
What type of normalization does removeBatchEffect function require as the input?
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 3 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 3 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
2
votes
2
replies
625
views
Batch correction for DE analysis
batch-correction
mRNA
RNA-seq
DEGs
MDSplot
updated 3 days ago by
Ram
43k • written 2.6 years ago by
Yoonji
▴ 10
5
votes
2
replies
1.7k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq
batch
batch-effect
sequencing
updated 3 days ago by
Ram
43k • written 2.9 years ago by
Mat
▴ 60
0
votes
0
replies
1.4k
views
Help with Circos plot "Assumption Error" that prevents plotting a protein interactions network
CircosPlot
updated 3 days ago by
Ram
43k • written 3.3 years ago by
hniels01
• 0
0
votes
0
replies
728
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq
scRNA-Seq
batch-effect
updated 1 day ago by
Ram
43k • written 3.4 years ago by
hkarakurt
▴ 180
2
votes
0
replies
1.8k
views
ComBat-seq adjustment of batch effects
RNA-Seq
ComBat-seq
SVA
edgeR
batch-effect
updated 3 days ago by
Ram
43k • written 3.4 years ago by
chatterjee.arumoy
▴ 50
156 results • Page
2 of 4
Recent Votes
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Answer: Cellranger count error: Input FASTQ file ended prematurely
Answer: RNA seq differential expression analysis
Answer: MEGA Analysis Issue on High-Performance Computer
Comment: Ciriquant not configuring hisat2 indexed files
bcftools multiple commands
bcftools pipe generated file from first command with second
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Comment: Free/open source 23andme-like analysis
by
swbarnes2
14k
Accurately assessing a few QC metrics is trivially easy. Assessing the significance of variants in a clinically responsible way is really…
Comment: Cellranger count error: Input FASTQ file ended prematurely
by
swbarnes2
14k
If _1 and _2 really are the same library, you should rename the fastqs, or make symlinks, such that they have the same sample name, but dif…
Comment: Cellranger count error: Input FASTQ file ended prematurely
by
ATpoint
81k
Just delete the index read files. They just take up space and will never be used.
Comment: Adding CB tag to bam file
by
swbarnes2
14k
Yes. Why wouldn't you use, say, AddOrReplaceReadsGroups?
Comment: Ciriquant not configuring hisat2 indexed files
by
Atul K.
• 0
Thank you. Decreased the threads to 2 (changed the threads: 2 in the config file; but it was somehow using 4). It did run for sometime but …
Answer: GTF file from Stringtie to R Studio for either Ballgown or DESeq2
by
Ram
43k
See this section on how to use tximport to import StringTie output for DESeq2 processing: https://bioconductor.org/packages/devel/bioc/vign…
Comment: how to find genes that are significantly expressed in brain cortex samples
by
Ram
43k
Can you explain the normalization or give me a link that describes it, please? Comparison across samples will always be caveated as RNA-seq…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
Sorry, I see how harsh I come across. It's not good practice to use multiple versions of R in the same project. I can understand legacy pro…
Answer: MEGA Analysis Issue on High-Performance Computer
by
Mensur Dlakic
★ 27k
> I have ensured that I am using the latest version of MEGA and that other applications are not consuming excessive resources during the an…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★ 1.7k
Some of us are still learning and fall foul to knowledge limitation fairly regularly. Luckily we have people to put us in our place.
Answer: Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
by
GenoMax
141k
> I know that I should be able to collect protein sequences from the blastp results into a file, but I do not know how to do this. You c…
Comment: how to find genes that are significantly expressed in brain cortex samples
by
rheab1230
▴ 140
I got the normalized gene count from gtex portal. they use inverse quantile normalization
Comment: what's the genomic location and name of gene responsible for orange and black pa
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Matthias Zepper
4.5k
It is not entirely off, but evidently also not correct. Melanin biosynthesis is a multistep process, that indeed prominently involves the…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
> so a single Rscript could utilise multiple environments and versions How is that sane, let alone "better"? Also, why use `snap` for curl…
Comment: how to find genes that are significantly expressed in brain cortex samples
by
Ram
43k
Normalized how?
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