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527 results • Page
2 of 11
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Votes
Replies
0
votes
0
replies
136
views
what exactly is a k-mer table (remora)?
remora
basecall
3 days ago by
anne
• 0
1
vote
1
reply
158
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
1 day 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
364
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
2 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
172
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
190
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
130
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
190
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
162
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
128
views
Automated internal stop codon checker
ORF
stopcodon
internal
virus
4 days ago by
Balazs Horvath
▴ 10
0
votes
0
replies
130
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
141
views
FreeBayes detection capacity
reads
freebayes
long
4 days ago by
quentinperriere
• 0
0
votes
2
replies
214
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
2 days ago by
DKA
▴ 40
0
votes
2
replies
237
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 5 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 5 days ago by
Jiang
• 0
0
votes
0
replies
177
views
Core SNP tree VS. concatenated core genome tree
phylogenetic
tree
SNP
6 days ago by
YiweiZhu
▴ 30
0
votes
0
replies
188
views
Somatic and Germline variant calling for tumor, normal and blood sample
germline
variants
somatic
updated 6 days ago by
Ram
43k • written 6 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
0
votes
0
replies
175
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 7 days ago by
GenoMax
141k • written 7 days ago by
zec018
• 0
0
votes
0
replies
187
views
SeuratDisk: including "counts" dataset in conversion to AnnData
Seurat
SeuratDisk
AnnData
updated 7 days ago by
Ram
43k • written 7 days ago by
roussine
▴ 10
0
votes
0
replies
173
views
I am getting more annotation hits from HOMER than I have actual peaks. Is that normal?
ATAC-seq
HOMER
7 days ago by
Ronin
• 0
4
votes
13
replies
783
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
2
votes
1
reply
236
views
VEP annotation --per_gene allele choice
VEP
updated 7 days ago by
Ram
43k • written 7 days ago by
atariw
▴ 10
0
votes
2
replies
269
views
Are GeneExpression Subtype annotations removed from TCGA-GBM?
tcga-gbm
subtyping
tcga
updated 7 days ago by
Zhenyu Zhang
★ 1.2k • written 7 days ago by
Apollonia
• 0
1
vote
1
reply
236
views
RNA seq normalization and gene gene correlation
rna-seq
pearson-correlation
vst
updated 7 days ago by
Ram
43k • written 7 days ago by
Fish
• 0
0
votes
0
replies
179
views
Snakemake fails to find conda in PBS
snakemake
7 days ago by
yixinzeng
• 0
0
votes
0
replies
184
views
KaryoPlot: Gene coverage over centromeric regions
Gene
coverage
Centromere
Bedtools
7 days ago by
Mary
• 0
0
votes
0
replies
173
views
Protein stability analysis
mutation
analysis
7 days ago by
marco.barr
▴ 60
1
vote
4
replies
373
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 7 days ago by
Morteza
• 0
3
votes
1
reply
255
views
how to change the gene header names in a fasta file?
fasta
bioawk
awk
seqkit
updated 8 days ago by
Ram
43k • written 8 days ago by
rj.rezwan
• 0
0
votes
0
replies
160
views
Multiple Spike-Ins
MeRIP
Spike-In
8 days ago by
Adam
▴ 20
0
votes
0
replies
158
views
Tools for Sequence Consensus
Consensus-Sequence
bacteria
updated 8 days ago by
Ram
43k • written 8 days ago by
Reno
• 0
2
votes
2
replies
265
views
DepMap: siRNA and CRSIPR discrepancy
DepMap
updated 8 days ago by
ATpoint
81k • written 8 days ago by
Shicheng Guo
★ 9.4k
1
vote
0
replies
149
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
8 days ago by
eesiribloom
▴ 80
0
votes
3
replies
299
views
10x GEX and ADT data analysis in Seurat
Seurat
scRNA-seq
ADT
Cite-seq
GEX
updated 6 days ago by
ATpoint
81k • written 8 days ago by
gdfsnkfns
• 0
0
votes
4
replies
294
views
Questions about transfering wgs file to reference genome file
fasta
cram
genome
8 days ago by
me
• 0
0
votes
2
replies
251
views
WGCNA
PCA
WGCNA
EIGENGENE
7 days ago by
rajasekargutha
▴ 60
527 results • Page
2 of 11
Recent Votes
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
C: How to setup a Summarized Experiment
A: How to download genome assemblies from NCBI with a list of GCA identifiers?
what's the genomic location and name of gene responsible for orange and black patches in calico cats
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★ 2.4k
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▴ 70
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GenoMax
141k
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Shicheng Guo
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Recent Replies
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
by
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?
Comment: Duplicate marking, read names, and the SRA
by
GenoMax
141k
With public data one has to work with what is there. If the information about position is absent then only thing that could be done is to l…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★ 1.7k
Or better yet. To have an R package that allows access to conda environments via "conda list env" so that environments can be switched with…
Comment: what's the genomic location and name of gene responsible for orange and black pa
by
GenoMax
141k
If GPT is right then it says that: > The specific gene responsible for the orange and non-orange (black or > gray) fur colors in cats is t…
Comment: what's the genomic location and name of gene responsible for orange and black pa
by
Jean-Karim Heriche
27k
As far as I know the Orange locus hasn't been mapped to a gene. Maybe this paper will help in narrowing the search: https://www.ncbi.nlm.ni…
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