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0 votes
3 replies
1.8K views
Are there any preferred trajectory/pseudotime analyses that do not require an arbitrary start point?
scrna-seq pseudotime monocle scvelo trajectory-analysis
written by nathansuek • nathansuek
0 votes
23 replies
5.2K views
error with Tximport when txOut = TRUE
tximport r
updated by Ram Ram • written by mbansal • mbansal
0 votes
1 reply
770 views
UMI tools to extract Paired end miRNA reads
paired umi_extract
updated by biofalconch biofalconch • written by otieno43 • otieno43
0 votes
1 reply
989 views
Discrepancy Between Genus and Phylum Level Results in ANCOMBC2
differential-abundance
updated by andres.firrincieli andres.firrincieli • written by benkosta • benkosta
0 votes
1 reply
1.1K views
Differential binding analysis between different TFs
differential-binding chip-seq transcription-factor
updated by Ming Tommy Tang Ming Tommy Tang • written by Alexandra • Alexandra
1 vote
0 replies
960 views
News: St. Jude Graduate School of Biomedical Sciences Launch of MS ABDS Program
education
written by rachel.mccollough • rachel.mccollough
4 votes
0 replies
26K views
Herald: The Biostar Herald for Friday, November 01, 2024
herald
written by Biostar Biostar
0 votes
0 replies
539 views
Why does the normal tissue increase while I try to select the tumor purity great than 60%
tumor-purity tcga
updated by Ram Ram • written by nuorain • nuorain
0 votes
4 replies
2.0K views
Seurat - unordered cells
r seurat
written by solo.albif • solo.albif
0 votes
1 reply
880 views
GISTIC 2.0 parameter change not happening
cnv gistic
updated by Ram Ram • written by Swattik • Swattik
0 votes
1 reply
1.1K views
How to find the adapter sequence of an RNAseq dataset?
fastqc trimming adapter rnaseq
updated by GenoMax GenoMax • written by Maryam • Maryam
0 votes
4 replies
1.4K views
Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
single-cell
updated by Ram Ram • written by wangziwei0010 • wangziwei0010
0 votes
2 replies
982 views
Repeat CT in overrepresented sequences
scrna fastqc overrepresented sequences
updated by allingt • allingt • written by Analeigh • Analeigh
0 votes
1 reply
868 views
Can a read be aligned more than once?
alignment gaf read sam
updated by GenoMax GenoMax • written by guntul • guntul
0 votes
6 replies
2.2K views
What is a genomic range that would almost always get decent WGS coverage but is never covered by WES?
wes wgs
updated by i.sudbery i.sudbery • written by Jeremy Leipzig Jeremy Leipzig
0 votes
1 reply
1.3K views
Using NumReads column of quants.genes.sf file to build DESeq2 input
r deseq2 rna-seq salmon
updated by i.sudbery i.sudbery • written by Ezequiel • Ezequiel
0 votes
1 reply
725 views
SCE object acting strangley
r sce seurat singlecellexperiment
updated by Ram Ram • written by wykpenguin • wykpenguin
0 votes
5 replies
1.8K views
why I get "Running twoBitToFa failed" when loading chopchop
chopchop twobittofa crispr
updated by GenoMax GenoMax • written by WYZ1120zzh • WYZ1120zzh
0 votes
0 replies
998 views
TCGA differential DNA methylation analysis 450K best practices
methylation hm450k differential
written by Brassicka • Brassicka
0 votes
3 replies
1.2K views
Conversion from .lib to .faa file
fasta blast
updated by Ram Ram • written by watermicrogirl • watermicrogirl
0 votes
2 replies
1.1K views
Inquiry about depth of coverage and copy number variation
number copy cnv sequencing depth variation
written by Chen • Chen
0 votes
1 reply
821 views
Finding Differential Phosphosites in TMT Phosphoproteomics Data
deqms mass phosphoproteomics proteomics spec
updated by ATpoint ATpoint • written by jesswhitts • jesswhitts
0 votes
1 reply
976 views
Magnesium ion in a post-docking adjustment
docking magnesium ion
updated by dthorbur dthorbur • written by Rodolfo Adrián • Rodolfo Adrián
0 votes
4 replies
1.9K views
R encountering fatal error and quitting the session
r randomforestsrc random-forest
updated by Dunois • Dunois • written by anjalivasudevan98 • anjalivasudevan98
0 votes
1 reply
955 views
scRNA seq dissimilarity plot
anosim scrna-seq dissimilarity
updated by Bastien Hervé Bastien Hervé • written by carolofharvest • carolofharvest
0 votes
6 replies
2.2K views
dittoHeatmap; adding column labels on the heatmap
pheatmap complexheatmap dittoheatmap
updated by jared.andrews07 jared.andrews07 • written by Varun Gupta Varun Gupta
0 votes
3 replies
1.5K views
IDAT to FASTA workflow
plink r idat fasta gwas
updated by GenoMax GenoMax • written by sabrilo171 • sabrilo171
0 votes
7 replies
2.4K views
GATK - Output differences in Calls when Split by chromosome intervals and without splitting
gatk picard mergevcf vcftools
written by Maverick • Maverick
0 votes
0 replies
809 views
mageck mle design matrix
crispr mageck-mle design-matrix pooled-screen
written by Assa Yeroslaviz Assa Yeroslaviz
0 votes
2 replies
1.6K views
After subsetting a seurat object number of variable features is wrong.
findvariablefeatures seurat subset
updated by Ram Ram • written by Assa Yeroslaviz Assa Yeroslaviz
0 votes
1 reply
987 views
PyDeseq2 - InvalidIndexError
python rna-seq pandas pydeseq2 deseq2
updated by Dunois • Dunois • written by tmanjonas • tmanjonas
0 votes
0 replies
998 views
Finding the IC50 from GraphPad Prism
ic50
written by camiinnocente • camiinnocente
0 votes
0 replies
501 views
Pipelines for CAZenzymes, COG, KO, MetaCyc, Pfam and TIGRFAM analysis
picrust2 metagenomic micfunpred
updated by Ram Ram • written by Petrônio • Petrônio
0 votes
1 reply
1.1K views
Gene performance/coverage calculation methodology in .bam files using samtools
samtools ngs coverage
updated by Ram Ram • written by slzr_ • slzr_
1 vote
3 replies
2.6K views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
rna-seq cibersortx deconvolution cibersort
updated by jurriaanjanssen • jurriaanjanssen • written by star • star
0 votes
12 replies
9.5K views
Error in CIBERSORTx
rna-seq cibersort lm22
updated by jurriaanjanssen • jurriaanjanssen • written by Manav • Manav
0 votes
5 replies
28K views
PC3 & PC2 using plotPCA function in R
r plotpca pca
updated by Ram Ram • written by User000 User000
0 votes
0 replies
516 views
(vg rna) some transcripts have multiple projections on haplotypes and abnormal length growth
vg
written by Wenhai • Wenhai
0 votes
1 reply
1.0K views
Minor Allele Frequency Calculation for 23andMe data
maf gwas pgs
updated by barslmn • barslmn • written by Priyatam • Priyatam
0 votes
2 replies
993 views
De novo assembly with more genome size than expected
illumina sequencing assembly genomics
updated by GenoMax GenoMax • written by Isidro • Isidro
0 votes
2 replies
2.0K views
Why use Hi-C and/or Bionano for scaffolding when Nanopore sequencing exists?
wgs hic sequencing nanopore genomics
updated by shelkmike shelkmike • written by Mark • Mark
0 votes
7 replies
3.0K views
HTSeq-count vs. FeatureCounts: Significant Difference in Results
featurecounts htseq-count
written by Dora • Dora
1 vote
0 replies
597 views
Enironmental metabolic ability - metagenomic assembly or MAGs
mags environmental microbiology metagenomes
updated by GenoMax GenoMax • written by sipeskm • sipeskm
12 votes
5 replies
4.0K views
Tutorial: removeBatchEffect explained using base R linear models
removebatcheffects limma batch-effect
updated by SamGG • SamGG • written by nhaus • nhaus
1 vote
6 replies
3.4K views
Question: can not obtain DESeq2 results
rna-seq deseq2
updated by Jack • Jack • written by zjxia • zjxia
1 vote
0 replies
433 views
Stable coordinates in gaf files?
gfa gaf rgfa
written by Uveyik • Uveyik
0 votes
2 replies
1.6K views
Dealing with outliers for differential expression in proteomics
proteomics pca dea outliers limma
updated by ATpoint ATpoint • written by Jorge HB • Jorge HB
0 votes
1 reply
723 views
Differential expression genes(downstream analysis)
bulk-rnaseq
updated by pinheirofabiano • pinheirofabiano • written by odi • odi
0 votes
1 reply
992 views
RNAhybrid + svm_light for miRNA target prediction
microrna svm target rnahybrid
updated by bingyanzheng18 • bingyanzheng18 • written by Lucrezia • Lucrezia
0 votes
0 replies
657 views
How do I set the RNAhybrid parameters to get more accurate and as many results as possible
rnahybrid mirna_target_genes_prediction
written by bingyanzheng18 • bingyanzheng18
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